Script | Spoken-Tutorial - User contributions [en]

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-06-06T08:12:04Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
||
* In microsecond or millisecond timescale, ligand binding or folding is studied.
* These are computationally intensive processes
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| '''Slide Number 9'''

'''Timescale of Protein Motions'''
||
* In microsecond or millisecond timescale, ligand binding or folding is studied.
* These are computationally intensive processes
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| '''Slide Number 10'''

'''Timescale of Protein Motions'''
||
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the '''production md run'''.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type, '''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 11'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyze flexible structures or molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 12'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 13'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 14'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 15'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 16'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 17'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 18'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 19'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-05-30T08:26:22Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
||
* In microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| '''Slide Number 9'''

'''Timescale of Protein Motions'''
||
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the '''production md run'''.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type, '''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyze flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 10'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 11'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 12'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 13'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 14'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 15'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-05-30T08:17:38Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
||
* In microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| '''Slide Number 9'''

'''Timescale of Protein Motions'''
||
* Use a high performance computation facility or a '''GPU''' for longer calculations

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the '''production md run'''.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type, '''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyze flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-05-30T07:36:17Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
||
* In microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes.
* Use a high performance computation facility or a '''GPU''' for longer calculations.

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the '''firstmd''' directory, where the files are saved.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the production md run.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''-r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type,

'''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyse flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-05-30T07:33:41Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
|| * The microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes.
* Use a high performance computation facility or a '''GPU''' for longer calculations.

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the '''firstmd''' directory, where the files are saved.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the production md run.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''-r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type,

'''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyse flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-05-30T07:32:28Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
|| * The microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes.
* Use a high performance computation facility or a '''GPU''' for longer calculations.

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the '''firstmd''' directory, where the files are saved.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the production md run.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''-r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type,

'''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyse flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-05-30T07:31:58Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1 nanosecond production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
|| * The microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes.
* Use a high performance computation facility or a '''GPU''' for longer calculations.

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the '''firstmd''' directory, where the files are saved.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the production md run.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''-r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type,

'''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyse flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Visualization-With-VMD/English

2022-05-30T06:18:12Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Visualization With VMD''' of '''Gromacs''' generated files.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn to,

* Open a '''Gromacs''' generated trajectory file
* Play and view the frames in the trajectory
* Color and display structures from selected frames

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| |
* Create a movie from the trajectory
* Align structures from two different states of the protein

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''VMD''' 1.9.3
* '''VLC''' media player 3.0.8

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial,
* Learner must be familiar with basics of '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided folder with input files to the '''Desktop''' directory.
| | Copy the provided folder containing the input files to the working directory.

'''VMD''' can open the '''trr, gro''' and '''pdb''' files present here.

|-
| | Show input files in the file manager.
| | The '''npt.trr''' is a trajectory file, which is readable by '''VMD'''.

This file was generated in the pressure equilibration step.

It contains the many conformational states of the protein during the simulation.

|-
| |
| | Let’s open the '''npt.gro''' file in '''VMD'''.

|-
||Showm opening a '''terminal''', changing to working directory and
||Linux users, can open a terminal and change to the working directory.

Windows users must first open '''VMD'''.

|-
| | Type '''VMD npt.gro''' at the terminal prompt.

Press '''Enter'''.
| | Open a '''terminal''' and change path to the working directory.

The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.

|-
| | The molecule '''npt.gro''' gets loaded.
| | This is the starting structure file for the '''MD''' simulation of the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Let’s change the display mode and show only the '''protein''' for clarity.

|-
| | In the '''Selected atoms''' form, type '''protein''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''protein'''.

Now water molecules get hidden.

|-
| | For '''Drawing method''', choose '''Ribbons'''.
| | For '''Drawing method''', choose '''Ribbons'''.

|-
| | In the '''VMD''' terminal enter the command '''pbc box'''.
| | I will also display the box with the '''pbc space box''' command.

|-
| | Show '''VMD''' graphics window.
| | Let’s ascertain the protein is not split into parts in the box.

It may happen so and due to the '''periodic boundary condition'''.

|-
| |
| | If such a situation is observed, user must rerun the equilibration step.

|-
| | Click on '''File, New Molecule'''.
| | Let’s next load the trajectory file.

Click on '''File, New Molecule'''.

|-
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
| | In the '''Load Files for''' pulldown, choose '''npt.gro'''.

Let's load the the '''trajectory''' file '''npt.trr'''.

|-
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.

|-
| | Close the '''Load''' window.
| | Let’s close the '''Load''' window.

The trajectory file is loaded to a structure by '''VMD'''.

|-
| | Show loading of all the states.

Show number of frames in the '''Main window'''.
| | '''VMD''' loads all the conformational states of the protein from the '''trajectory''' file.

These are called the different frames.

The number of frames or states, in the '''trajectory''' is also displayed here.

|-
| | Click on the play button.
| | Next, click on the play button, seen on the lower right end of the main window.

|-
| | Show the playing of the trajectory.
| | Notice, all the states in the trajectory being played.

|-
| | Play the trajectory.
| | The duration of the '''equilibration''' step is short.

|-
| | Slide the speed slider to slow it down.
| | We can also adjust the speed at which the states are played.

|-
| | Click on pause and step buttons.
| | We can pause and step through the states of the trajectory as seen here.

|-
| | Click on '''Graphics, Representations'''.
| | Now, let’s view the chloride ions, which are present in the system .

For this, first click on '''Graphics, Representations'''.

|-
| | Click on '''Create New rep'''.
| | Then, click on '''Create New rep'''.

|-
| | In the '''Selected atoms''' form, type '''name CL''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''name CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.

Close the '''Representations''' window.
| | For '''Drawing methods''', choose '''beads'''.

Close the '''Representations''' window.

Notice the 8 chloride ions.

|-
| | Play the trajectory again.
| | Now, play the '''trajectory''' file again.

|-
| |
| | Notice that, the '''chloride''' ions, being smaller, moves faster than the protein.

This movement is due to diffusion.

|-
| | Show the ion exiting the box and being added back.
| | Occasionally, an ion exits the box and it gets added back to the box.

This is due to the '''periodic boundary condition''' which was set up in the '''mdp''' file.

|-
| |
| | Let’s make a movie of all the frames in the trajectory.

|-
| | Click on '''Extensions, Visualization''' and choose '''Movie Maker'''.
| | For this click on '''Extensions, Visualization''' and choose '''Movie Maker'''.

|-
| | The '''VMD Movie Generator''' window opens.
| | The '''VMD Movie Generator''' window opens.

|-
| | Click on '''Set working directory'''.

In the dialog box, change to '''Videos''' folder.
| | I will first '''Set the working directory'''. Click on it.

In the dialog box, change to the '''Videos''' path to save the videos.

You may choose this directory as you desire.

|-
| | Click on '''Movie settings''' and choose '''Trajectory'''.
| | Click on '''Movie settings''' and choose '''Trajectory'''.

|-
| | Click on '''Format''' and choose '''MPEG-2 (ffmpeg)'''.
| | Click on '''Format''' and choose '''MPEG-2''' '''(ffmpeg)''' to choose the video format.

|-
| | Click on '''Renderer''' and hover over '''Snapshot'''.
| | For '''Renderer''' I will retain '''Snapshot'''.

This captures each frame as seen in the graphics window.

|-
| | In '''Name of movie''' field, type '''firstmovie'''.
| | For '''Name of movie''', I will enter '''firstmovie'''.

|-
| | Hover over '''trajectory''' step and duration.
| | Notice, the '''trajectory''' step is 1 and movie duration is 4 seconds now.

I will retain the defaults.

|-
| | Click on '''Make Movie'''.
| | Click on '''Make Movie''' and notice the progress.

|-
| | Close the '''VMD Movie Generator''' window.
| | After the process is completed, close the '''VMD Movie Generator''' window.

|-
| | Open file manager and go to the '''Videos''' folder.
| | Open the file manager and go to the '''Videos''' folder where the movie was created.

|-
| | Open the '''firstmovie.mpg''' file.
| | Open the '''firstmovie.mpg'''.

I will use '''VLC''' media player for it.

|-
| | Play the '''firstvideo.mpg''' video.
| | Pause the tutorial video and play the movie that you just created.

|-
| | Close '''VLC''' and go back to '''VMD'''.
| | I will close '''VLC''' and let’s go back to '''VMD'''.

|-
| | Open the graphical representations window.
| | Next, let’s display color and select frames for display from the trajectory.

Go to the graphical representations window.

|-
| | Show '''Selected atoms''' form with '''npt.gro''' molecule selected.
| | Make sure that the '''npt.gro''' molecule is selected as seen.

|-
| | In the Coloring methods pulldown, select '''Trajectory''' and choose'''Timestep'''.
| | In the '''Coloring method''' pulldown, select '''Trajectory''' and choose
'''Timestep'''.

|-
| | Cursor on '''Drawing method'''.

Click on the play button in '''VMD''' main window.
| | You may change the '''Drawing method''' if desired.

Now, play the '''trajectory'''.

|-
| | Show color change in the graphics window.
| | Notice the starting frame is red by default and ending frame is in blue color.

|-
| | Click on play again to stop.
| | I will stop to play the frames.

|-
| | Go to '''Representations''', and select the '''Trajectory''' tab.
| | Go to '''Representations''', and select the '''Trajectory''' tab.

|-
| | Cursor on '''Draw multiple frames'''.
| | By default, '''Draw multiple frames''' is set to '''now''', which is the current frame.

|-
| | Type, '''0:20:102''' in the '''Draw multiple frames''' form.
| | To show every 20 frames, type 0 colon 20 colon 102.

My '''trajectory''' range is 0 to 102 and hence the limits are specified.

|-
| | Show the 5 displayed frames.
| | Now, notice the 5 frames that are displayed in the graphical window.

|-
| |
| | Next, let’s choose specific user selected frames for display.

|-
| | In the '''Draw multiple frames''' form, Type, '''1 and 49 and 100''' and press '''Enter'''.
| | Say I want to display, 1st, 49th and 100 th frame only.

Type, '''1 and 49 and 100''' and press '''Enter''' as seen here.

|-
| | Show the displayed frames in graphical window.
| | This will show the three specified frames.

|-
| |
| | Let’s compare the '''npt.gro''' structure with the starting structure of '''first.gro'''.

We will read both molecules and align them for comparison.

|-
| | In the '''Draw multiple frames''' form, Type, '''now''' and press '''Enter'''.
| | First I will reset the display to the present frame.

Then alignment process will be clearly visible.

|-
| |Close the Window.
| | Close the representations Windows.

|-
| | Click on '''File, New Molecule'''.

Click on '''Browse''', choose '''first.gro'''.

Click on '''Ok''' and then on '''Load'''.
| | Let’s read in '''first.gro'''.

'''First.gro''' has hydrogens added to it.

It’s precursor is, '''1aki.pdb'''.

Both molecules have the same number of atoms in the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Click on '''Graphics, Representations'''.

|-
| | Choose the '''protein representation'''.
| | Choose the '''protein representation'''.

|-
| | For '''Drawing method''', choose '''Lines'''.
| | For '''Drawing method''', choose '''Lines'''.

Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.

|-
| | Rotate the graphics window to show both the molecules.
| | Then, the loaded structures may not be discernible separately.

If so, rotate them in the graphics window to view them.

|-
| | Cursor on the graphics windows.
| | Now the molecules are not aligned properly, to view any conformational differences.

Hence, we will align the two molecules or overlay them .

|-
| | Click on '''Extensions''' and '''Tk console'''.
| | For this first click on '''Extensions''' and '''Tk console'''.

A '''VMD TKconsole''' window opens.

|-
| | Type, '''set sel0 [atomselect 0 protein] '''and press '''Enter'''.
| | Type the command as seen and press '''Enter'''.

This selects all atoms in the protein from the first structure.

|-
| | Type, '''set sel1 [atomselect 1 protein] '''and press '''Enter'''.
| | Now select all the atoms from the second structure using the command as seen.

|-
| | Type, '''set A [measure fit $sel0 $sel1]''' and press '''Enter'''.
| | This command '''fits''' the positions of the atoms in the two protein molecules.

The '''fit''' command works, only when the number of atoms are the same.

|-
| | Type, '''$sel0 move $A''' and press '''Enter'''.
| | The move command, '''realigns''' the position of the molecule in the graphics window.

The coordinates of the first molecule is aligned with that of the second.

|-
| | Cursor in '''VMD''' graphics window.
| | The change in positions and conformational change if any is clearly seen.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we,

* Loaded a trajectory file
* Played and viewed frames from the '''trajectory'''
* Created a movie using the frames in the '''trajectory'''

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Changed color and viewed selected frames
* Aligned the starting and equilibrated structures of the protein

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

Answer the following question.* Can '''1AKI.pdb''' be aligned with '''npt.gro''', with the '''measure fit''' command?
* Explain the reasoning and demonstrate it

|-
| | '''Slide Number 10'''

'''Assignment'''
| | * Create a new representation for '''npt.gro''' molecule
* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
* This displays water molecules present only within 2A of protein

|-
| | '''Slide Number 11'''

'''Assignment'''
| | * Play the trajectory and notice the movement of water molecules

|-
| | '''Slide Number 12'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 13'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 14'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 15'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Visualization-With-VMD/English

2022-05-26T11:35:39Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Visualization With VMD''' of '''Gromacs''' generated files.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn to,

* Open a '''Gromacs''' generated trajectory file
* Play and view the frames in the trajectory
* Color and display structures from selected frames

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| |
* Create a movie from the trajectory
* Align structures from two different states of the protein

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''VMD''' 1.9.3
* '''VLC''' media player 3.0.8

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial,
* Learner must be familiar with basics of '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided folder with input files to the '''Desktop''' directory.
| | Copy the provided folder containing the input files to the working directory.

'''VMD''' can open the '''trr, gro''' and '''pdb''' files present here.

|-
| | Show input files in the file manager.
| | The '''npt.trr''' is a trajectory file, which is readable by '''VMD'''.

This file was generated in the pressure equilibration step.

It contains the many conformational states of the protein during the simulation.

|-
| |
| | Let’s open the '''npt.gro''' file in '''VMD'''.

|-
||Showm opening a '''terminal''', changing to working directory and
||Linux users, can open a terminal and change to the working directory.

Windows users must first open '''VMD'''.

|-
| | Type '''VMD npt.gro''' at the terminal prompt.

Press '''Enter'''.
| | Open a '''terminal''' and change path to the working directory.

The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.

|-
| | The molecule '''npt.gro''' gets loaded.
| | This is the starting structure file for the '''MD''' simulation of the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Let’s change the display mode and show only the '''protein''' for clarity.

|-
| | In the '''Selected atoms''' form, type '''protein''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''protein'''.

Now water molecules get hidden.

|-
| | For '''Drawing method''', choose '''Ribbons'''.
| | For '''Drawing method''', choose '''Ribbons'''.

|-
| | In the '''VMD''' terminal enter the command '''pbc box'''.
| | I will also display the box with the '''pbc space box''' command.

|-
| | Show '''VMD''' graphics window.
| | Let’s ascertain the protein is not split into parts in the box.

It may happen so and due to the '''periodic boundary condition'''.

|-
| |
| | If such a situation is observed, user must rerun the equilibration step.

|-
| | Click on '''File, New Molecule'''.
| | Let’s next load the trajectory file.

Click on '''File, New Molecule'''.

|-
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
| | In the '''Load Files for''' pulldown, choose '''npt.gro'''.

Let's load the the '''trajectory''' file '''npt.trr'''.

|-
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.

|-
| | Close the '''Load''' window.
| | Let’s close the '''Load''' window.

The trajectory file is loaded to a structure by '''VMD'''.

|-
| | Show loading of all the states.

Show number of frames in the '''Main window'''.
| | '''VMD''' loads all the conformational states of the protein from the '''trajectory''' file.

These are called the different frames.

The number of frames or states, in the '''trajectory''' is also displayed here.

|-
| | Click on the play button.
| | Next, click on the play button, seen on the lower right end of the main window.

|-
| | Show the playing of the trajectory.
| | Notice, all the states in the trajectory being played.

|-
| | Play the trajectory.
| | The duration of the '''equilibration''' step is short.

|-
| | Slide the speed slider to slow it down.
| | We can also adjust the speed at which the states are played.

|-
| | Click on pause and step buttons.
| | We can pause and step through the states of the trajectory as seen here.

|-
| | Click on '''Graphics, Representations'''.
| | Now, let’s view the chloride ions, which are present in the system .

For this, first click on '''Graphics, Representations'''.

|-
| | Click on '''Create New rep'''.
| | Then, click on '''Create New rep'''.

|-
| | In the '''Selected atoms''' form, type '''name CL''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''name CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.

Close the '''Representations''' window.
| | For '''Drawing methods''', choose '''beads'''.

Close the '''Representations''' window.

Notice the 8 chloride ions.

|-
| | Play the trajectory again.
| | Now, play the '''trajectory''' file again.

|-
| |
| | Notice that, the '''chloride''' ions, being smaller, moves faster than the protein.

This movement is due to diffusion.

|-
| | Show the ion exiting the box and being added back.
| | Occasionally, an ion exits the box and it gets added back to the box.

This is due to the '''periodic boundary condition''' which was set up in the '''mdp''' file.

|-
| |
| | Let’s make a movie of all the frames in the trajectory.

|-
| | Click on '''Extensions, Visualization''' and choose '''Movie Maker'''.
| | For this click on '''Extensions, Visualization''' and choose '''Movie Maker'''.

|-
| | The '''VMD Movie Generator''' window opens.
| | The '''VMD Movie Generator''' window opens.

|-
| | Click on '''Set working directory'''.

In the dialog box, change to '''Videos''' folder.
| | I will first '''Set the working directory'''. Click on it.

In the dialog box, change to the '''Videos''' path to save the videos.

You may choose this directory as you desire.

|-
| | Click on '''Movie settings''' and choose '''Trajectory'''.
| | Click on '''Movie settings''' and choose '''Trajectory'''.

|-
| | Click on '''Format''' and choose '''MPEG-2 (ffmpeg)'''.
| | Click on '''Format''' and choose '''MPEG-2''' '''(ffmpeg)''' to choose the video format.

|-
| | Click on '''Renderer''' and hover over '''Snapshot'''.
| | For '''Renderer''' I will retain '''Snapshot'''.

This captures each frame as seen in the graphics window.

|-
| | In '''Name of movie''' field, type '''firstmovie'''.
| | For '''Name of movie''', I will enter '''firstmovie'''.

|-
| | Hover over '''trajectory''' step and duration.
| | Notice, the '''trajectory''' step is 1 and movie duration is 4 seconds now.

I will retain the defaults.

|-
| | Click on '''Make Movie'''.
| | Click on '''Make Movie''' and notice the progress.

|-
| | Close the '''VMD Movie Generator''' window.
| | After the process is completed, close the '''VMD Movie Generator''' window.

|-
| | Open file manager and go to the '''Videos''' folder.
| | Open the file manager and go to the '''Videos''' folder where the movie was created.

|-
| | Open the '''firstmovie.mpg''' file.
| | Open the '''firstmovie.mpg'''.

I will use '''VLC''' media player for it.

|-
| | Play the '''firstvideo.mpg''' video.
| | Pause the tutorial video and play the movie that you just created.

|-
| | Close '''VLC''' and go back to '''VMD'''.
| | I will close '''VLC''' and let’s go back to '''VMD'''.

|-
| | Open the graphical representations window.
| | Next, let’s display color and select frames for display from the trajectory.

Go to the graphical representations window.

|-
| | Show '''Selected atoms''' form with '''npt.gro''' molecule selected.
| | Make sure that the '''npt.gro''' molecule is selected as seen.

|-
| | In the Coloring methods pulldown, select '''Trajectory''' and choose'''Timestep'''.
| | In the '''Coloring method''' pulldown, select '''Trajectory''' and choose
'''Timestep'''.

|-
| | Cursor on '''Drawing method'''.

Click on the play button in '''VMD''' main window.
| | You may change the '''Drawing method''' if desired.

Now, play the '''trajectory'''.

|-
| | Show color change in the graphics window.
| | Notice the starting frame is red by default and ending frame is in blue color.

|-
| | Click on play again to stop.
| | I will stop to play the frames.

|-
| | Go to '''Representations''', and select the '''Trajectory''' tab.
| | Go to '''Representations''', and select the '''Trajectory''' tab.

|-
| | Cursor on '''Draw multiple frames'''.
| | By default, '''Draw multiple frames''' is set to '''now''', which is the current frame.

|-
| | Type, '''0:20:102''' in the '''Draw multiple frames''' form.
| | To show every 20 frames, type 0 colon 20 colon 102.

My '''trajectory''' range is 0 to 102 and hence the limits are specified.

|-
| | Show the 5 displayed frames.
| | Now, notice the 5 frames that are displayed in the graphical window.

|-
| |
| | Next, let’s choose specific user selected frames for display.

|-
| | In the '''Draw multiple frames''' form, Type, '''1 and 49 and 100''' and press '''Enter'''.
| | Say I want to display, 1st, 49th and 100 th frame only.

Type, '''1 and 49 and 100''' and press '''Enter''' as seen here.

|-
| | Show the displayed frames in graphical window.
| | This will show the three specified frames.

|-
| |
| | Let’s compare the '''npt.gro''' structure with the starting structure of '''first.gro'''.

We will read both molecules and align them for comparison.

|-
| | In the '''Draw multiple frames''' form, Type, '''now''' and press '''Enter'''.
| | First I will reset the display to the present frame.

Then alignment process will be clearly visible.

|-
| | Click on '''File, New Molecule'''.

Click on '''Browse''', choose '''first.gro'''.

Click on '''Ok''' and then on '''Load'''.
| | Let’s read in '''first.gro'''.

|-
| |Close the Window.
| | Close the representations Windows.

'''First.gro''' has hydrogens added to it.

It’s precursor is, '''1aki.pdb'''.

Both molecules have the same number of atoms in the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Click on '''Graphics, Representations'''.

|-
| | Choose the '''protein representation'''.
| | Choose the '''protein representation'''.

|-
| | For '''Drawing method''', choose '''Lines'''.
| | For '''Drawing method''', choose '''Lines'''.

Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.

|-
| | Rotate the graphics window to show both the molecules.
| | Then, the loaded structures may not be discernible separately.

If so, rotate them in the graphics window to view them.

|-
| | Cursor on the graphics windows.
| | Now the molecules are not aligned properly, to view any conformational differences.

Hence, we will align the two molecules or overlay them .

|-
| | Click on '''Extensions''' and '''Tk console'''.
| | For this first click on '''Extensions''' and '''Tk console'''.

A '''VMD TKconsole''' window opens.

|-
| | Type, '''set sel0 [atomselect 0 protein] '''and press '''Enter'''.
| | Type the command as seen and press '''Enter'''.

This selects all atoms in the protein from the first structure.

|-
| | Type, '''set sel1 [atomselect 1 protein] '''and press '''Enter'''.
| | Now select all the atoms from the second structure using the command as seen.

|-
| | Type, '''set A [measure fit $sel0 $sel1]''' and press '''Enter'''.
| | This command '''fits''' the positions of the atoms in the two protein molecules.

The '''fit''' command works, only when the number of atoms are the same.

|-
| | Type, '''$sel0 move $A''' and press '''Enter'''.
| | The move command, '''realigns''' the position of the molecule in the graphics window.

The coordinates of the first molecule is aligned with that of the second.

|-
| | Cursor in '''VMD''' graphics window.
| | The change in positions and conformational change if any is clearly seen.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we,

* Loaded a trajectory file
* Played and viewed frames from the '''trajectory'''
* Created a movie using the frames in the '''trajectory'''

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Changed color and viewed selected frames
* Aligned the starting and equilibrated structures of the protein

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

Answer the following question.* Can '''1AKI.pdb''' be aligned with '''npt.gro''', with the '''measure fit''' command?
* Explain the reasoning and demonstrate it

|-
| | '''Slide Number 10'''

'''Assignment'''
| | * Create a new representation for '''npt.gro''' molecule
* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
* This displays water molecules present only within 2A of protein

|-
| | '''Slide Number 11'''

'''Assignment'''
| | * Play the trajectory and notice the movement of water molecules

|-
| | '''Slide Number 12'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 13'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 14'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 15'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Visualization-With-VMD/English

2022-05-26T08:18:22Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Visualization With VMD''' of '''Gromacs''' generated files.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn to,

* Open a '''Gromacs''' generated trajectory file
* Play and view the frames in the trajectory
* Color and display structures from selected frames

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| |
* Create a movie from the trajectory
* Align structures from two different states of the protein

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''VMD''' 1.9.3
* '''VLC''' media player 3.0.8

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial,
* Learner must be familiar with basics of '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided folder with input files to the '''Desktop''' directory.
| | Copy the provided folder containing the input files to the working directory.

'''VMD''' can open the '''trr, gro''' and '''pdb''' files present here.

|-
| | Show input files in the file manager.
| | The '''npt.trr''' is a trajectory file, which is readable by '''VMD'''.

This file was generated in the pressure equilibration step.

It contains the many conformational states of the protein during the simulation.

|-
| |
| | Let’s open the '''npt.gro''' file in '''VMD'''.

|-
||Showm opening a '''terminal''', changing to working directory and
||Linux users, can open a terminal and change to the working directory.

Windows users must first open '''VMD'''.

|-
| | Type '''VMD npt.gro''' at the terminal prompt.

Press '''Enter'''.
| | Open a '''terminal''' and change path to the working directory.

The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.

|-
| | The molecule '''npt.gro''' gets loaded.
| | This is the starting structure file for the '''MD''' simulation of the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Let’s change the display mode and show only the '''protein''' for clarity.

|-
| | In the '''Selected atoms''' form, type '''protein''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''protein'''.

Now water molecules get hidden.

|-
| | For '''Drawing method''', choose '''Ribbons'''.
| | For '''Drawing method''', choose '''Ribbons'''.

|-
| | In the '''VMD''' terminal enter the command '''pbc box'''.
| | I will also display the box with the '''pbc space box''' command.

|-
| | Show '''VMD''' graphics window.
| | Let’s ascertain the protein is not split into parts in the box.

It may happen so and due to the '''periodic boundary condition'''.

|-
| |
| | If such a situation is observed, user must rerun the equilibration step.

|-
| | Click on '''File, New Molecule'''.
| | Let’s next load the trajectory file.

Click on '''File, New Molecule'''.

|-
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
| | In the '''Load Files for''' pulldown, choose '''npt.gro'''.

Let's load the the '''trajectory''' file '''npt.trr'''.

|-
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.

|-
| | Close the '''Load''' window.
| | Let’s close the '''Load''' window.

The trajectory file is loaded to a structure by '''VMD'''.

|-
| | Show loading of all the states.

Show number of frames in the '''Main window'''.
| | '''VMD''' loads all the conformational states of the protein from the '''trajectory''' file.

These are called the different frames.

The number of frames or states, in the '''trajectory''' is also displayed here.

|-
| | Click on the play button.
| | Next, click on the play button, seen on the lower right end of the main window.

|-
| | Show the playing of the trajectory.
| | Notice, all the states in the trajectory being played.

|-
| | Play the trajectory.
| | The duration of the '''equilibration''' step is short.

|-
| | Slide the speed slider to slow it down.
| | We can also adjust the speed at which the states are played.

|-
| | Click on pause and step buttons.
| | We can pause and step through the states of the trajectory as seen here.

|-
| | Click on '''Graphics, Representations'''.
| | Now, let’s view the chloride ions, which are present in the system .

For this, first click on '''Graphics, Representations'''.

|-
| | Click on '''Create New rep'''.
| | Then, click on '''Create New rep'''.

|-
| | In the '''Selected atoms''' form, type '''name CL''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''name CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.

Close the '''Representations''' window.
| | For '''Drawing methods''', choose '''beads'''.

Close the '''Representations''' window.

Notice the 8 chloride ions.

|-
| | Play the trajectory again.
| | Now, play the '''trajectory''' file again.

|-
| |
| | Notice that, the '''chloride''' ions, being smaller, moves faster than the protein.

This movement is due to diffusion.

|-
| | Show the ion exiting the box and being added back.
| | Occasionally, an ion exits the box and it gets added back to the box.

This is due to the '''periodic boundary condition''' which was set up in the '''mdp''' file.

|-
| |
| | Let’s make a movie of all the frames in the trajectory.

|-
| | Click on '''Extensions, Visualization''' and choose '''Movie Maker'''.
| | For this click on '''Extensions, Visualization''' and choose '''Movie Maker'''.

|-
| | The '''VMD Movie Generator''' window opens.
| | The '''VMD Movie Generator''' window opens.

|-
| | Click on '''Set working directory'''.

In the dialog box, change to '''Videos''' folder.
| | I will first '''Set the working directory'''. Click on it.

In the dialog box, change to the '''Videos''' path to save the videos.

You may choose this directory as you desire.

|-
| | Click on '''Movie settings''' and choose '''Trajectory'''.
| | Click on '''Movie settings''' and choose '''Trajectory'''.

|-
| | Click on '''Format''' and choose '''MPEG-2 (ffmpeg)'''.
| | Click on '''Format''' and choose '''MPEG-2''' '''(ffmpeg)''' to choose the video format.

|-
| | Click on '''Renderer''' and hover over '''Snapshot'''.
| | For '''Renderer''' I will retain '''Snapshot'''.

This captures each frame as seen in the graphics window.

|-
| | In '''Name of movie''' field, type '''firstmovie'''.
| | For '''Name of movie''', I will enter '''firstmovie'''.

|-
| | Hover over '''trajectory''' step and duration.
| | Notice, the '''trajectory''' step is 1 and movie duration is 4 seconds now.

I will retain the defaults.

|-
| | Click on '''Make Movie'''.
| | Click on '''Make Movie''' and notice the progress.

|-
| | Close the '''VMD Movie Generator''' window.
| | After the process is completed, close the '''VMD Movie Generator''' window.

|-
| | Open file manager and go to the '''Videos''' folder.
| | Open the file manager and go to the '''Videos''' folder where the movie was created.

|-
| | Open the '''firstmovie.mpg''' file.
| | Open the '''firstmovie.mpg'''.

I will use '''VLC''' media player for it.

|-
| | Play the '''firstvideo.mpg''' video.
| | Pause the tutorial video and play the movie that you just created.

|-
| | Close '''VLC''' and go back to '''VMD'''.
| | I will close '''VLC''' and let’s go back to '''VMD'''.

|-
| | Open the graphical representations window.
| | Next, let’s display color and select frames for display from the trajectory.

Go to the graphical representations window.

|-
| | Show '''Selected atoms''' form with '''npt.gro''' molecule selected.
| | Make sure that the '''npt.gro''' molecule is selected as seen.

|-
| | In the Coloring methods pulldown, select '''Trajectory''' and choose'''Timestep'''.
| | In the '''Coloring method''' pulldown, select '''Trajectory''' and choose
'''Timestep'''.

|-
| | Cursor on '''Drawing method'''.

Click on the play button in '''VMD''' main window.
| | You may change the '''Drawing method''' if desired.

Now, play the '''trajectory'''.

|-
| | Show color change in the graphics window.
| | Notice the starting frame is red by default and ending frame is in blue color.

|-
| | Click on play again to stop.
| | I will stop to play the frames.

|-
| | Go to '''Representations''', and select the '''Trajectory''' tab.
| | Go to '''Representations''', and select the '''Trajectory''' tab.

|-
| | Cursor on '''Draw multiple frames'''.
| | By default, '''Draw multiple frames''' is set to '''now''', which is the current frame.

|-
| | Type, '''0:20:102''' in the '''Draw multiple frames''' form.
| | To show every 20 frames, type 0 colon 20 colon 102.

My '''trajectory''' range is 0 to 102 and hence the limits are specified.

|-
| | Show the 5 displayed frames.
| | Now, notice the 5 frames that are displayed in the graphical window.

|-
| |
| | Next, let’s choose specific user selected frames for display.

|-
| | In the '''Draw multiple frames''' form, Type, '''1 and 49 and 100''' and press '''Enter'''.
| | Say I want to display, 1st, 49th and 100 th frame only.

Type, '''1 and 49 and 100''' and press '''Enter''' as seen here.

|-
| | Show the displayed frames in graphical window.
| | This will show the three specified frames.

|-
| |
| | Let’s compare the '''npt.gro''' structure with the starting structure of '''first.gro'''.

We will read both molecules and align them for comparison.

|-
| | In the '''Draw multiple frames''' form, Type, '''now''' and press '''Enter'''.
| | First I will reset the display to the present frame.

Then alignment process will be clearly visible.

|-
| | Click on '''File, New Molecule'''.

Click on '''Browse''', choose '''first.gro'''.

Click on '''Ok''' and then on '''Load'''.
| |

|-
| |Close the Window.
| | Close the representations Windows.

Let’s read in '''first.gro'''.

'''First.gro''' has hydrogens added to it.

It’s precursor, '''1aki.pdb'''.

Both molecules have the same number of atoms in the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Click on '''Graphics, Representations'''.

|-
| | Choose the '''protein representation'''.
| | Choose the '''protein representation'''.

|-
| | For '''Drawing method''', choose '''Lines'''.
| | For '''Drawing method''', choose '''Lines'''.

Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.

|-
| | Rotate the graphics window to show both the molecules.
| | The loaded structures may not be discernible separately.

If so, rotate them in the graphics window to view them.

|-
| | Cursor on the graphics windows.
| | Now the two molecules are not aligned with each other.

Hence possible conformational differences are not seen clearly.

Let’s align the two molecules or overlay them .

|-
| | Click on '''Extensions''' and '''Tk console'''.
| | For this first click on '''Extensions''' and '''Tk console'''.

A '''VMD TKconsole''' window opens.

|-
| | Type, '''set sel0 [atomselect 0 protein] '''and press '''Enter'''.
| | Type the command as seen and press '''Enter'''.

This selects all atoms in the protein from the first structure.

|-
| | Type, '''set sel1 [atomselect 1 protein] '''and press '''Enter'''.
| | Now select all the atoms from the second structure using the command as seen.

|-
| | Type, '''set A [measure fit $sel0 $sel1]''' and press '''Enter'''.
| | This command '''fits''' the positions of the atoms in the two protein molecules.

The '''fit''' command works, only when the number of atoms are the same.

|-
| | Type, '''$sel0 move $A''' and press '''Enter'''.
| | The move command, '''realigns''' the position of the molecule in the graphics window.

The coordinates of the first molecule is aligned with that of the second.

|-
| | Cursor in '''VMD''' graphics window.
| | The change in positions and conformational change if any is clearly seen.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we,

* Loaded a trajectory file
* Played and viewed frames from the '''trajectory'''
* Created a movie using the frames in the '''trajectory'''

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Changed color and viewed selected frames
* Aligned the starting and equilibrated structures of the protein

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

Answer the following question.* Can '''1AKI.pdb''' be aligned with '''npt.gro''', with the '''measure fit''' command?
* Explain the reasoning and demonstrate it

|-
| | '''Slide Number 10'''

'''Assignment'''
| | * Create a new representation for '''npt.gro''' molecule
* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
* This displays water molecules present only within 2A of protein

|-
| | '''Slide Number 11'''

'''Assignment'''
| | * Play the trajectory and notice the movement of water molecules

|-
| | '''Slide Number 12'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 13'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 14'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 15'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-03-08T11:00:13Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1ns production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
|| * The microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes.
* Use a high performance computation facility or a '''GPU''' for longer calculations.

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the '''firstmd''' directory, where the files are saved.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the production md run.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''-r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type,

'''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyse flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

File:Timescale-pae001.png

2022-03-08T10:58:51Z

Ranipv076:

Gromacs/C3/Production-Run-for-Lysozyme/English

2022-03-08T10:58:07Z

Ranipv076: Created page with " {| border=1 | | '''Visual Cue''' | | '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the spoken tutorial on '''Production Run for Lysozyme'''...."

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Production Run for Lysozyme'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will,
* Complete 1ns production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* Load the '''xtc''' file for trajectory
* Calculate '''RMSD''' from trajectory

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * Save data to various output files
* Align a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Show input files.

Show, copied, files in '''firsmd''' directory.
|| Several files are provided with this tutorial.

First, copy, the '''mdp''' file to the working directory.

If needed, copy the required files from the previous step.

|-
|| Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').

Type '''cd Documents/firstmd''' and press '''Enter'''.
|| Open a terminal and go to the working directory.

|-
|| Type '''cd ls''' and press '''Enter'''.
|| I will also list the files.

|-
|| Cursor on '''npt.gro''' and '''npt.tpr'''.
|| The structure and configuration files for '''MD''' simulation are '''npt.gro''' & '''npt.tpr'''.

At this point, the following has happened to the starting '''PDB''' file.

|-
|| Show all the files in the folder.
|| The protein is solvated, charge neutralized with ions and energy minimized.

Then, in the initial MD step, temperature and pressure was equilibrated.

This prepared the system for the Production run MD.

I have all the files from all the steps in this folder.

|-
|| Cursor on '''md.mdp''' and open in a text editor.
|| Open the '''mdp''' file provided for '''MD''' simulation in a text editor.

|-
|| Cursor on the time.
|| Here, the timescale of simulation is 1 '''ns'''.

|-
||
|| This allows us to follow changes in the conformation of the protein.

In energy minimization and equilibration steps, the time duration was shorter.

|-
|| Back to the text editor and close the '''mdp''' file.
|| Often, step size and length of simulation are adjusted.

This file specifies ½ million steps in 1 ns.

Frequency with which structures are written to the trajectory is also adjustable.

Let’s close the '''mdp''' file.

|-
|| '''Slide Number 7'''

'''Timescale of Protein Motions'''

[[Image:timescale-pae001.png|top|500px]]
|| This image shows the timescale of molecular motions we usually encounter.

The ns-ps time encompasses the lower end of protein motions for classical MD.

|-
|| '''Slide Number 8'''

'''Timescale of Protein Motions'''
|| * The microsecond or millisecond, ligand binding or folding is studied.
* These are computationally intensive processes.
* Use a high performance computation facility or a '''GPU''' for longer calculations.

|-
|| Go to the '''terminal'''.
|| Go to the '''terminal'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the '''firstmd''' directory, where the files are saved.

|-
|| Type, '''gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md-1.tpr''' and press '''Enter'''.
|| Enter the command as seen here to assemble the '''configuration''' for the '''md''' run.

'''npt.gro is''' the starting structure for the production md run.

|-
|| Cursor on '''md-1.tpr'''.
|| The '''tpr''' file is the output file from this step.

An '''-r''' flag is used if we need to restrain the protein conformation.

This is often done when studying protein-ligand binding.

Here we will not used it.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal''' to list the files.

Notice the output '''md-1.tpr''', that is created.

This prepared the system for the '''production md'''.

|-
|| Press '''Ctrl+L''' to clear the screen.
|| As we did for the energy minimization step, we will enter the next command.

|-
|| Type,

'''gmx mdrun -v -deffnm md-1''' and press '''Enter'''.
|| Enter the '''mdrun''' command as seen to start the '''production run'''.

Usually, molecular dynamics refers to equilibration followed by production run.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''verbose flag''' shows only a few details.

The number of steps and time needed to complete are seen on the screen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 500 thousand steps in 1 ns.

This process may take a day or so on many personal computers.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on.

Use the provided data for further analysis.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
|| Show files in the file manager.
|| Several files with '''md''' prefix are generated in the working directory.

|-
|| Highlight and delete the files to be deleted.
|| If you had aborted the process, delete the incomplete files that are created.

|-
||
|| If you have completed the process, do not delete the files.

A '''gro''' file will get created at the completion of the process.

|-
|| Show files to be copied from provided file.

Copy them to the working directory.
|| Copy the provided files with the '''md-1''' prefix to the working directory.

|-
|| Type '''ls -ltr''' and press '''Enter'''.
|| This step creates additional file types with '''cpt''' and '''xtc''' extensions.
|-
|| Cursor on '''md-1.xtc''' file.
|| The '''xtc''' file is a compressed trajectory file.

This file is useful, in data analysis during long simulations.
|-
|| Cursor on '''md.trr''', '''md.log''' and '''md.edr''' files.
|| '''Trr''', '''log''' and '''edr''' files are also created in this process.
|-
|| Show the output files.
|| In case of errors, learner may refer to the '''log''' file for trouble shooting.

|-
||
|| We have generated several files for further analysis.

Data analysis path varies depending on our aim or objective of simulation.

|-
|| '''Slide Number 9'''

'''Data Analysis'''
|| Few examples of data analysis are,
* Validation, visualization
* Analysis of energetics, H-bonding
* Secondary structure changes
* Ligand Binding, surface analysis,
* Analysis of subset of atoms in the system

|-
|| Open a web browser.

Go to, [https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html] .
|| Open a web browser.

Let’s go to the '''Gromacs''' manual site as seen here.

|-
|| Cursor on the left panel.
|| On the left frame notice the various categories of topics for analysis.

Atomic interactions, kinetics and '''PCA''' are also options.

These are useful to analyse flexible structures or ones such as molten globules.

|-
||
|| Learner is encouraged to read further on this to know more.

|-
|| Go to the '''terminal'''.

Press '''Ctrl+L'''.
|| Go to the terminal.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type, '''vmd md-1.gro md-1.xtc''' and press '''Enter'''.
|| Let’s open '''VMD''' to view the trajectory from the 1'''ns''' long simulation.

This time we will use the '''xtc''' file instead of the '''trr''' file to load the '''trajectory'''.

'''Xtc''' is a compressed format of the simulation trajectory.

'''Windows''' users must first open '''VMD'''.

Then open the '''gro''' file, followed by the '''xtc''' '''trajectory''' file.

|-
|| Click on '''Graphics, representation'''.

Type, '''protein''' for '''Selected atoms''' and press '''Enter'''.
|| Hiding the water molecules from graphics display will be useful for clarity.

|-
||
|| You may adjust the graphic representation of the protein to your desire.

I will change it to show as ribbons.

|-
|| In the '''VMD''' terminal enter the command '''pbc box'''.
|| Display the box, using the command as seen here in the '''vmd terminal'''.

|-
|| Play the trajectory.
|| Pause the video and play the trajectory.

Notice the '''xtc''' file has 1002 frames.

|-
||
|| Later on, you may load the '''trr''' file and notice, it has only 101 frames.

'''Xtc''' format has precision of 3 decimal places compared to 6 decimals for '''trr'''.

Hence, even though '''xtc''' has 10 times more frames, the file sizes are comparable.

|-
|| Stop playing the trajectory.

Close the Window.
|| Visualization alone is not sufficient to know the features of the data.

Hence let’s do few data analysis to see the features embedded.

|-
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.
|| Click on '''Extensions, Analysis''' and choose '''RMSD Trajectory Tool'''.

A '''RMSD trajectory tool''' window opens.

|-
||
|| Let’s calculate '''RMSD''' of the backbone atoms in the trajectory.

|-
|| In '''Selection modifiers''', check the box for '''Backbone'''.
|| In '''Selection modifiers''', check the box for '''Backbone'''.

Notice that, '''Trace''' or '''NH''' can also be selected for plotting.

|-
|| Cursor over trajectory section.
|| From the '''Trajectory''' section, we can also select a range of frames for analysis.

I will retain the defaults and check the boxes for '''Plot''' and '''Save'''.

|-
|| Cursor on '''trajrmsd.dat'''.
|| Notice that, the data will also get saved with the given filename.

You may change it if you desire.

I will leave it as is.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on the '''RMSD'''.

Show the graph.
|| Click on the '''RMSD''' button and the graph is seen.

'''X''' axis is the frame number and '''y''' axis is the '''RMSD''' in the graph.

|-
|| Click on '''File''' in graphics window.
|| We can also export the data in many different formats as seen here.

|-
|| Screenshot of the file manager and output file.
|| The data can also be written to a text file in two column format.

Learner may use a plotting program of your choice to plot it.

|-
|| Close the '''RMSD Trajectory Tool''' window.
|| Let’s close this window.

|-
|| Cursor on the graphics window.
|| Now, let’s display frame 50 and align it to '''md-1.gro'''.

|-
|| Close the '''RMSD''' graphical window.

Go to '''representations''' and click on '''Create Rep'''.
|| Let’s close this window.

Go to '''representations''' window and create a new representation.

|-
|| Go to the '''Trajectory''' tab.
|| Go to the '''Trajectory''' tab.

|-
|| Cursor on '''Draw multiple frames '''form, type, 50 and press '''Enter'''.
|| In the '''Draw multiple frames''' form, type 50 and press '''Enter'''.

This shows the 50th frame also.

|-
|| Open the '''RMSD Trajectory Tool'''.
|| To align them, go back to the '''RMSD Trajectory Tool'''.

|-
|| For '''Reference mol''', choose '''Selected'''.
|| For '''Reference mol''', choose '''Selected'''.

|-
|| Type 50 for '''Reference frame'''.
|| Type 50 for '''Reference frame'''.

|-
|| Uncheck the the box for '''Plot'''.
|| I will uncheck the box for '''Plot'''.

|-
|| Click on '''md-1.gro''' in '''mol''' section.
|| In the molecule section, click on '''md-1.gro''' file to select it.

|-
|| Click on '''ALIGN'''.

Show alignment in the graphical window.
|| Now, click on '''ALIGN''' and notice the two aligned molecules.

|-
|| Click on '''FIle, Save Visualization State'''.

In the '''filename''' form, type filename '''analysis.vmd''' and click on '''Ok'''.
|| Click on '''FIle, Save Visualization State''' to save the state in '''VMD'''.

Enter file name '''analysis.vmd''' and retain the working directory to save the file.

|-
|| Show the '''Options''' menu.
|| Pause the video and explore the '''Options''' menu.

Various file formats and options are available for user convenience.

|-
|| Screenshot of '''energy''' command options to export to '''xvg''' file.
|| You may further, extract and plot more parameters.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we,

* Completed 1ns Production run for '''lysozyme'''
* About timescales of motions
* Time taken for simulation
* About output data and various types of data analysis

|-
|| '''Slide Number 10'''

'''Summary'''
|| * Loaded the '''xtc''' trajectory file
* About '''RMSD trajectory tool''' and analysis
* Aligned a frame in the trajectory with a reference molecule

|-
|| '''Slide Number 11'''

'''Assignment'''
|| For assignment activity, please do the following.

* Open the '''log''' file and go through the details
* Plot '''RMSD''' of '''trace''' (C-alpha) atoms only
* Create '''Ramachandran''' plot of the lowest and highest energy structure

|-
|| '''Slide Number 12'''

'''Assignment'''
|| Using the '''energy '''command,

* Plot '''solvent accessible surface area''' ('''SASA''')
* Explore '''gmxcheck''', and '''ngmx''' commands

|-
|| '''Slide Number 13'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 14'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 15'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 16'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-21T14:09:08Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp file to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 femtoseconds.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system configuration from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''pressure dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Performed '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation and checked for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands starting from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-21T12:15:53Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp file to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 femtoseconds.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system configuration from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Performed '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation and checked for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands starting from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-21T10:00:14Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp file to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 femtoseconds.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Performed '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation and checked for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands starting from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-21T09:02:28Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp file to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 femtoseconds.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Performed '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation and checked for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-18T09:10:35Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp file to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 femtoseconds.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-18T09:09:50Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 femtoseconds.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-02-18T09:06:49Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 fs.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300 '''Kelvin'''.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional '''gro''' file will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Visualization-With-VMD/English

2022-02-01T08:57:17Z

Ranipv076:

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Visualization With VMD''' of '''Gromacs''' generated files.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn to,

* Open a '''Gromacs''' generated trajectory file
* Play and view the frames in the trajectory
* Color and display structures from selected frames

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| |
* Create a movie from the trajectory
* Align structures from two different states of the protein

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''VMD''' 1.9.3
* '''VLC''' media player 3.0.8

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial,
* Learner must be familiar with basics of '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided folder with input files to the '''Desktop''' directory.
| | Copy the provided folder containing the input files to the working directory.

'''VMD''' can open the '''trr, gro''' and '''pdb''' files present here.

|-
| | Show input files in the file manager.
| | The '''npt.trr''' is a trajectory file, which is readable by '''VMD'''.

This file was generated in the pressure equilibration step.

It contains the many conformational states of the protein during the simulation.

|-
| |
| | Let’s open the '''npt.gro''' file in '''VMD'''.

|-
| | Open a '''terminal'''.

Type '''VMD npt.gro''' at the terminal prompt.

Press '''Enter'''.
| | Open a '''terminal''' and change path to the working directory.

The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.

|-
| | The molecule '''npt.gro''' gets loaded.
| | This is the starting structure file for the '''MD''' simulation of the protein.

Text annotation: Windows users must open '''VMD''' first, then open the '''gro''' file through '''VMD'''.

|-
| | Click on '''Graphics, Representations'''.
| | Let’s change the display mode and show only the '''protein''' for clarity.

|-
| | In the '''Selected atoms''' form, type '''protein''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''protein'''.

Now water molecules get hidden.

|-
| | For '''Drawing method''', choose '''Ribbons'''.
| | For '''Drawing method''', choose '''Ribbons'''.

|-
| | In the '''VMD''' terminal enter the command '''pbc box'''.
| | I will also display the box with the '''pbc space box''' command.

|-
| | Show '''VMD''' graphics window.
| | Let’s ascertain the protein is not split into parts in the box.

It may happen so and due to the '''periodic boundary condition'''.

|-
| |
| | If such a situation is observed, user must rerun the equilibration step.

|-
| | Click on '''File, New Molecule'''.
| | Let’s next load the trajectory file.

Click on '''File, New Molecule'''.

|-
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.

|-
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.

|-
| | Close the '''Load''' window.
| | Let’s close the '''Load''' window.

The trajectory file is loaded to a structure by '''VMD'''.

|-
| | Show loading of all the states.

Show number of frames in the '''Main window'''.
| | '''VMD''' loads all the conformational states of the protein from the '''trajectory''' file.

These are called the different frames.

The number of frames or states, in the '''trajectory''' is also displayed here.

|-
| | Click on the play button.
| | Next, click on the play button, seen on the lower right end of the main window.

|-
| | Show the playing of the trajectory.
| | Notice, all the states in the trajectory being played.

|-
| | Play the trajectory.
| | The duration of the '''equilibration''' step is short.

|-
| | Slide the speed slider to slow it down.
| | We can also adjust the speed at which the states are played.

|-
| | Click on pause and step buttons.
| | We can pause and step through the states of the trajectory as seen here.

|-
| | Click on '''Graphics, Representations'''.
| | Now, let’s view the chloride ions, which are present in the system .

For this, first click on '''Graphics, Representations'''.

|-
| | Click on '''Create New rep'''.
| | Then, click on '''Create New rep'''.

|-
| | In the '''Selected atoms''' form, type '''name CL''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''name CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.

Close the '''Representations''' window.
| | For '''Drawing methods''', choose '''beads'''.

Close the '''Representations''' window.

Notice the 8 chloride ions.

|-
| | Play the trajectory again.
| | Now, play the '''trajectory''' file again.

|-
| |
| | Notice that, the '''chloride''' ions, being smaller, moves faster than the protein.

This movement is due to diffusion.

|-
| | Show the ion exiting the box and being added back.
| | Occasionally, an ion exits the box and it gets added back to the box.

This is due to the '''periodic boundary condition''' which was set up in the '''mdp''' file.

|-
| |
| | Let’s make a movie of all the frames in the trajectory.

|-
| | Click on '''Extensions, Visualization''' and choose '''Movie Maker'''.
| | For this click on '''Extensions, Visualization''' and choose '''Movie Maker'''.

|-
| | The '''VMD Movie Generator''' window opens.
| | The '''VMD Movie Generator''' window opens.

|-
| | Click on '''Set working directory'''.

In the dialog box, change to '''Videos''' folder.
| | I will first '''Set the working directory'''. Click on it.

In the dialog box, change to the '''Videos''' path to save the videos.

You may choose this directory as you desire.

|-
| | Click on '''Movie settings''' and choose '''Trajectory'''.
| | Click on '''Movie settings''' and choose '''Trajectory'''.

|-
| | Click on '''Format''' and choose '''MPEG-2 (ffmpeg)'''.
| | Click on '''Format''' and choose '''MPEG-2''' '''(ffmpeg)''' to choose the video format.

|-
| | Click on '''Renderer''' and hover over '''Snapshot'''.
| | For '''Renderer''' I will retain '''Snapshot'''.

This captures each frame as seen in the graphics window.

|-
| | In '''Name of movie''' field, type '''firstmovie'''.
| | For '''Name of movie''', I will enter '''firstmovie'''.

|-
| | Hover over '''trajectory''' step and duration.
| | Now, the '''trajectory''' step is 1 and movie duration is 4 seconds now.

I will retain the defaults.

|-
| | Click on '''Make Movie'''.
| | Click on '''Make Movie''' and notice the progress.

|-
| | Close the '''VMD Movie Generator''' window.
| | After the process is completed, close the '''VMD Movie Generator''' window.

|-
| | Open file manager and go to the '''Videos''' folder.
| | Open the file manager and go to the '''Videos''' folder where the movie was created.

|-
| | Open the '''firstmovie.mpg''' file.
| | Open the '''firstmovie.mpg''' file.

I will use '''VLC''' media player for it.

|-
| | Play the '''firstvideo.mpg''' video.
| | Pause the tutorial video and play the movie that you just created.

|-
| | Close '''VLC''' and go back to '''VMD'''.
| | I will close '''VLC''' and let’s go back to '''VMD'''.

|-
| | Open the graphical representations window.
| | Next, let’s display color and select frames for display from the trajectory.

Go to the graphical representations window.

|-
| | Show '''Selected atoms''' form with '''npt.gro''' molecule selected.
| | Make sure that the '''npt.gro''' molecule is selected as seen.

|-
| | In the Coloring methods pulldown, select '''Trajectory''' and choose'''Timestep'''.
| | In the '''Coloring method''' pulldown, select '''Trajectory''' and choose
'''Timestep'''.

|-
| | Cursor on '''Drawing method'''.

Click on the play button in '''VMD''' main window.
| | You may change the '''Drawing method''' if desired.

Now, play the '''trajectory'''.

|-
| | Show color change in the graphics window.
| | Notice the starting frame is red by default and ending frame is in blue color.

|-
| | Click on play again to stop.
| | I will stop to play the frames.

|-
| | Go to '''Representations''', and select the '''Trajectory''' tab.
| | Go to '''Representations''', and select the '''Trajectory''' tab.

|-
| | Cursor on '''Draw multiple frames'''.
| | By default, '''Draw multiple frames''' is set to '''now''', which is the current frame.

|-
| | Type, '''0:20:102''' in the '''Draw multiple frames''' form.
| | To show every 20 frames, type 0 colon 20 colon 102.

My '''trajectory''' range is 0 to 102 and hence the limits are specified.

|-
| | Show the 5 displayed frames.
| | Now, notice the 5 frames that are displayed in the graphical window.

|-
| |
| | Next, let’s choose specific user selected frames for display.

|-
| | In the '''Draw multiple frames''' form, Type, '''1 and 49 and 100''' and press '''Enter'''.
| | Say I want to display, 1st, 49th and 100 th frame only.

In the form, type, '''1 and 49 and 100''' and press '''Enter''' as seen.

|-
| | Show the displayed frames in graphical window.
| | This will show the three specified frames.

|-
| |
| | Let’s compare the '''npt.gro''' structure with the starting structure of '''first.gro'''.

We will read both molecules and align them for comparison.

|-
| | In the '''Draw multiple frames''' form, Type, '''now''' and press '''Enter'''.
| | First I will reset the display to the present frame.

Then alignment process will be clearly visible.

|-
| | Click on '''File, New Molecule'''.

Click on '''Browse''', choose '''first.gro'''.

Click on '''Ok''' and then on '''Load'''.

Close the Window.
| | Close the representations Windows.

Let’s read in '''first.gro'''.

'''First.gro''' has hydrogens added to it.

It’s precursor, '''1aki.pdb'''.

Both molecules have the same number of atoms in the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Click on '''Graphics, Representations'''.

|-
| | Choose the '''protein representation'''.
| | Choose the '''protein representation'''.

|-
| | For '''Drawing method''', choose '''Lines'''.
| | For '''Drawing method''', choose '''Lines'''.

Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.

|-
| | Rotate the graphics window to show both the molecules.
| | The loaded structures may not be discernible separately.

If so, rotate them in the graphics window to view them.

|-
| | Cursor on the graphics windows.
| | Now the two molecules are not aligned with each other.

Hence possible conformational differences are not seen clearly.

Let’s align the two molecules or overlay them .

|-
| | Click on '''Extensions''' and '''Tk console'''.
| | For this first click on '''Extensions''' and '''Tk console'''.

A '''VMD TKconsole''' window opens.

|-
| | Type, '''set sel0 [atomselect 0 protein] '''and press '''Enter'''.
| | Type the command as seen and press '''Enter'''.

This selects all atoms in the protein from the first structure.

|-
| | Type, '''set sel1 [atomselect 1 protein] '''and press '''Enter'''.
| | Now select all the atoms from the second structure using the command as seen.

|-
| | Type, '''set A [measure fit $sel0 $sel1]''' and press '''Enter'''.
| | This command '''fits''' the positions of the atoms in the two protein molecules.

The '''fit''' command works, only when the number of atoms are the same.

|-
| | Type, '''$sel0 move $A''' and press '''Enter'''.
| | The move command, '''realigns''' the position of the molecule in the graphics window.

The coordinates of the first molecule is aligned with that of the second.

|-
| | Cursor in '''VMD''' graphics window.
| | The change in positions and conformational change if any is clearly seen.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we,

* Loaded a trajectory file
* Played and viewed frames from the '''trajectory'''
* Created a movie using the frames in the '''trajectory'''

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Changed color and viewed selected frames
* Aligned the starting and equilibrated structures of the protein

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

Answer the following question.* Can '''1AKI.pdb''' be aligned with '''npt.gro''', with the '''measure fit''' command?
* Explain the reasoning and demonstrate it

|-
| | '''Slide Number 10'''

'''Assignment'''
| | * Create a new representation for '''npt.gro''' molecule
* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
* This displays water molecules present only within 2A of protein

|-
| | '''Slide Number 11'''

'''Assignment'''
| | * Play the trajectory and notice the movement of water molecules

|-
| | '''Slide Number 12'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 13'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 14'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 15'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Visualization-With-VMD/English

2022-02-01T08:56:55Z

Ranipv076: Created page with "{| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Visualization With VMD''' of '''Gromac..."

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Visualization With VMD''' of '''Gromacs''' generated files.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn to,

* Open a '''Gromacs''' generated trajectory file
* Play and view the frames in the trajectory
* Color and display structures from selected frames

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| |
* Create a movie from the trajectory
* Align structures from two different states of the protein

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''VMD''' 1.9.3
* '''VLC''' media player 3.0.8

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial, * Learner must be familiar with basics of '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided folder with input files to the '''Desktop''' directory.
| | Copy the provided folder containing the input files to the working directory.

'''VMD''' can open the '''trr, gro''' and '''pdb''' files present here.

|-
| | Show input files in the file manager.
| | The '''npt.trr''' is a trajectory file, which is readable by '''VMD'''.

This file was generated in the pressure equilibration step.

It contains the many conformational states of the protein during the simulation.

|-
| |
| | Let’s open the '''npt.gro''' file in '''VMD'''.

|-
| | Open a '''terminal'''.

Type '''VMD npt.gro''' at the terminal prompt.

Press '''Enter'''.
| | Open a '''terminal''' and change path to the working directory.

The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.

|-
| | The molecule '''npt.gro''' gets loaded.
| | This is the starting structure file for the '''MD''' simulation of the protein.

Text annotation: Windows users must open '''VMD''' first, then open the '''gro''' file through '''VMD'''.

|-
| | Click on '''Graphics, Representations'''.
| | Let’s change the display mode and show only the '''protein''' for clarity.

|-
| | In the '''Selected atoms''' form, type '''protein''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''protein'''.

Now water molecules get hidden.

|-
| | For '''Drawing method''', choose '''Ribbons'''.
| | For '''Drawing method''', choose '''Ribbons'''.

|-
| | In the '''VMD''' terminal enter the command '''pbc box'''.
| | I will also display the box with the '''pbc space box''' command.

|-
| | Show '''VMD''' graphics window.
| | Let’s ascertain the protein is not split into parts in the box.

It may happen so and due to the '''periodic boundary condition'''.

|-
| |
| | If such a situation is observed, user must rerun the equilibration step.

|-
| | Click on '''File, New Molecule'''.
| | Let’s next load the trajectory file.

Click on '''File, New Molecule'''.

|-
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.

|-
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.

|-
| | Close the '''Load''' window.
| | Let’s close the '''Load''' window.

The trajectory file is loaded to a structure by '''VMD'''.

|-
| | Show loading of all the states.

Show number of frames in the '''Main window'''.
| | '''VMD''' loads all the conformational states of the protein from the '''trajectory''' file.

These are called the different frames.

The number of frames or states, in the '''trajectory''' is also displayed here.

|-
| | Click on the play button.
| | Next, click on the play button, seen on the lower right end of the main window.

|-
| | Show the playing of the trajectory.
| | Notice, all the states in the trajectory being played.

|-
| | Play the trajectory.
| | The duration of the '''equilibration''' step is short.

|-
| | Slide the speed slider to slow it down.
| | We can also adjust the speed at which the states are played.

|-
| | Click on pause and step buttons.
| | We can pause and step through the states of the trajectory as seen here.

|-
| | Click on '''Graphics, Representations'''.
| | Now, let’s view the chloride ions, which are present in the system .

For this, first click on '''Graphics, Representations'''.

|-
| | Click on '''Create New rep'''.
| | Then, click on '''Create New rep'''.

|-
| | In the '''Selected atoms''' form, type '''name CL''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''name CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.

Close the '''Representations''' window.
| | For '''Drawing methods''', choose '''beads'''.

Close the '''Representations''' window.

Notice the 8 chloride ions.

|-
| | Play the trajectory again.
| | Now, play the '''trajectory''' file again.

|-
| |
| | Notice that, the '''chloride''' ions, being smaller, moves faster than the protein.

This movement is due to diffusion.

|-
| | Show the ion exiting the box and being added back.
| | Occasionally, an ion exits the box and it gets added back to the box.

This is due to the '''periodic boundary condition''' which was set up in the '''mdp''' file.

|-
| |
| | Let’s make a movie of all the frames in the trajectory.

|-
| | Click on '''Extensions, Visualization''' and choose '''Movie Maker'''.
| | For this click on '''Extensions, Visualization''' and choose '''Movie Maker'''.

|-
| | The '''VMD Movie Generator''' window opens.
| | The '''VMD Movie Generator''' window opens.

|-
| | Click on '''Set working directory'''.

In the dialog box, change to '''Videos''' folder.
| | I will first '''Set the working directory'''. Click on it.

In the dialog box, change to the '''Videos''' path to save the videos.

You may choose this directory as you desire.

|-
| | Click on '''Movie settings''' and choose '''Trajectory'''.
| | Click on '''Movie settings''' and choose '''Trajectory'''.

|-
| | Click on '''Format''' and choose '''MPEG-2 (ffmpeg)'''.
| | Click on '''Format''' and choose '''MPEG-2''' '''(ffmpeg)''' to choose the video format.

|-
| | Click on '''Renderer''' and hover over '''Snapshot'''.
| | For '''Renderer''' I will retain '''Snapshot'''.

This captures each frame as seen in the graphics window.

|-
| | In '''Name of movie''' field, type '''firstmovie'''.
| | For '''Name of movie''', I will enter '''firstmovie'''.

|-
| | Hover over '''trajectory''' step and duration.
| | Now, the '''trajectory''' step is 1 and movie duration is 4 seconds now.

I will retain the defaults.

|-
| | Click on '''Make Movie'''.
| | Click on '''Make Movie''' and notice the progress.

|-
| | Close the '''VMD Movie Generator''' window.
| | After the process is completed, close the '''VMD Movie Generator''' window.

|-
| | Open file manager and go to the '''Videos''' folder.
| | Open the file manager and go to the '''Videos''' folder where the movie was created.

|-
| | Open the '''firstmovie.mpg''' file.
| | Open the '''firstmovie.mpg''' file.

I will use '''VLC''' media player for it.

|-
| | Play the '''firstvideo.mpg''' video.
| | Pause the tutorial video and play the movie that you just created.

|-
| | Close '''VLC''' and go back to '''VMD'''.
| | I will close '''VLC''' and let’s go back to '''VMD'''.

|-
| | Open the graphical representations window.
| | Next, let’s display color and select frames for display from the trajectory.

Go to the graphical representations window.

|-
| | Show '''Selected atoms''' form with '''npt.gro''' molecule selected.
| | Make sure that the '''npt.gro''' molecule is selected as seen.

|-
| | In the Coloring methods pulldown, select '''Trajectory''' and choose'''Timestep'''.
| | In the '''Coloring method''' pulldown, select '''Trajectory''' and choose
'''Timestep'''.

|-
| | Cursor on '''Drawing method'''.

Click on the play button in '''VMD''' main window.
| | You may change the '''Drawing method''' if desired.

Now, play the '''trajectory'''.

|-
| | Show color change in the graphics window.
| | Notice the starting frame is red by default and ending frame is in blue color.

|-
| | Click on play again to stop.
| | I will stop to play the frames.

|-
| | Go to '''Representations''', and select the '''Trajectory''' tab.
| | Go to '''Representations''', and select the '''Trajectory''' tab.

|-
| | Cursor on '''Draw multiple frames'''.
| | By default, '''Draw multiple frames''' is set to '''now''', which is the current frame.

|-
| | Type, '''0:20:102''' in the '''Draw multiple frames''' form.
| | To show every 20 frames, type 0 colon 20 colon 102.

My '''trajectory''' range is 0 to 102 and hence the limits are specified.

|-
| | Show the 5 displayed frames.
| | Now, notice the 5 frames that are displayed in the graphical window.

|-
| |
| | Next, let’s choose specific user selected frames for display.

|-
| | In the '''Draw multiple frames''' form, Type, '''1 and 49 and 100''' and press '''Enter'''.
| | Say I want to display, 1st, 49th and 100 th frame only.

In the form, type, '''1 and 49 and 100''' and press '''Enter''' as seen.

|-
| | Show the displayed frames in graphical window.
| | This will show the three specified frames.

|-
| |
| | Let’s compare the '''npt.gro''' structure with the starting structure of '''first.gro'''.

We will read both molecules and align them for comparison.

|-
| | In the '''Draw multiple frames''' form, Type, '''now''' and press '''Enter'''.
| | First I will reset the display to the present frame.

Then alignment process will be clearly visible.

|-
| | Click on '''File, New Molecule'''.

Click on '''Browse''', choose '''first.gro'''.

Click on '''Ok''' and then on '''Load'''.

Close the Window.
| | Close the representations Windows.

Let’s read in '''first.gro'''.

'''First.gro''' has hydrogens added to it.

It’s precursor, '''1aki.pdb'''.

Both molecules have the same number of atoms in the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Click on '''Graphics, Representations'''.

|-
| | Choose the '''protein representation'''.
| | Choose the '''protein representation'''.

|-
| | For '''Drawing method''', choose '''Lines'''.
| | For '''Drawing method''', choose '''Lines'''.

Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.

|-
| | Rotate the graphics window to show both the molecules.
| | The loaded structures may not be discernible separately.

If so, rotate them in the graphics window to view them.

|-
| | Cursor on the graphics windows.
| | Now the two molecules are not aligned with each other.

Hence possible conformational differences are not seen clearly.

Let’s align the two molecules or overlay them .

|-
| | Click on '''Extensions''' and '''Tk console'''.
| | For this first click on '''Extensions''' and '''Tk console'''.

A '''VMD TKconsole''' window opens.

|-
| | Type, '''set sel0 [atomselect 0 protein] '''and press '''Enter'''.
| | Type the command as seen and press '''Enter'''.

This selects all atoms in the protein from the first structure.

|-
| | Type, '''set sel1 [atomselect 1 protein] '''and press '''Enter'''.
| | Now select all the atoms from the second structure using the command as seen.

|-
| | Type, '''set A [measure fit $sel0 $sel1]''' and press '''Enter'''.
| | This command '''fits''' the positions of the atoms in the two protein molecules.

The '''fit''' command works, only when the number of atoms are the same.

|-
| | Type, '''$sel0 move $A''' and press '''Enter'''.
| | The move command, '''realigns''' the position of the molecule in the graphics window.

The coordinates of the first molecule is aligned with that of the second.

|-
| | Cursor in '''VMD''' graphics window.
| | The change in positions and conformational change if any is clearly seen.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we,

* Loaded a trajectory file
* Played and viewed frames from the '''trajectory'''
* Created a movie using the frames in the '''trajectory'''

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Changed color and viewed selected frames
* Aligned the starting and equilibrated structures of the protein

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

Answer the following question.* Can '''1AKI.pdb''' be aligned with '''npt.gro''', with the '''measure fit''' command?
* Explain the reasoning and demonstrate it

|-
| | '''Slide Number 10'''

'''Assignment'''
| | * Create a new representation for '''npt.gro''' molecule
* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
* This displays water molecules present only within 2A of protein

|-
| | '''Slide Number 11'''

'''Assignment'''
| | * Play the trajectory and notice the movement of water molecules

|-
| | '''Slide Number 12'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 13'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 14'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 15'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-01-08T17:52:12Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 fs.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300K.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
||
* Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional file '''gro''' will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 K.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-01-08T17:47:38Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 fs.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300K.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

Go through the '''Gromacs''' manual for detailed understanding.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
|| * Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional file '''gro''' will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 K.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-01-08T17:24:08Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 fs.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300K.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| If the r flag is used, then position must be restrained.

Pause the video and go through the additional materials section to know more.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
|| * Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional file '''gro''' will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 K.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2022-01-08T17:17:58Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 fs.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300K.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing them can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| The r flag is used only when position restraint is used in the '''mdp''' file.

Go through the additional materials section to know more.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
|| * Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional file '''gro''' will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 K.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Temperature-and-Pressure-Equilibration/English

2021-12-17T11:46:57Z

Ranipv076: Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the tutorial '''Temperature and Pressure Equilibration'''. |-..."

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Ensemble properties
* '''NVT''' and temperature equilibration
* Plot the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plot the pressure fluctuation

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''VMD''' 1.9.3
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial, * Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Copy the provided input files.

Cursor on '''nvt.mdp''' and '''npt.mdp'''.
|| Several files are provided with this tutorial.

Notice the two mdp files provided.

Copy the mdp files to the working directory.

|-
|| Cursor on N,V,T and P.
|| '''N''' stands for the number of particles present in the system.

'''V''' is for volume, '''T''' is for temperature and '''P''' is for pressure.

The number of particles and volume are constant for the system.

They are also user specified.

|-
|| '''Slide Number 6'''

'''Pressure and Temperature'''
||
* Pressure and temperature of the system
** Are macroscopic properties
** They fluctuate during the '''MD''' run
* They are calculated from the average velocity and position of the ensemble

|-
|| '''Slide Number 7'''

'''Pressure and Temperature'''
|| * Here, ensemble consists of all the particles in the system

|-
|| Show files in file manager for '''firstmd''' directory.

Open '''nvt.mdp''' in a text editor.
|| Let’s open the provided '''nvt.mdp''' file in a text editor.
|-
|| Show '''nvt.mdp''' in the text editor.

|| We will equilibrate the temperature of the system in the '''NVT''' step.

|-
|| Cursor on 100 ps.

Cursor on 50000 steps.
|| This is a short simulation for 100 ps with each step having 2 fs.

Hence there are 50000 steps.

This usually helps to stabilize the temperature of the system.
|-
|| Cursor on the file.
|| Diffusion effects are not significant over these timescales.

Often, step size and length of simulation are adjusted.

Here, the protein is not restrained.

Notice that, the line is not commented out with the semi colon.

|-
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
|| Here, temperature is set to 300K.

In this step there is no pressure equilibration.

|-
|| Close the '''mdp''' file.
|| Close the '''mdp''' file.

|-
|| Show website at, [https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html https://manual.gromacs.org/documentation/2019-current/reference-manual/special/remove-fast-dgf.html] '''
|| Details on choosing them can be accessed from the '''Gromacs''' documentation.

|-
||
|| Go through the '''Gromacs''' manual for detailed understanding of the parameters.

|-
| " |
|| In energy related studies '''NVT''' is important.

Protein-ligand binding studies is an example for this.

In mechanics related studies, '''NPT''' parameters are important.

|-
| " | Open '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
|| Let’s open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| Change to the working directory, where the files are saved.

|-
|| Type, '''gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr''' and press '''Enter'''.

Highlight '''em.gro'''.
|| Enter the command as seen here to construct the '''nvt.tpr''' file.

'''em.gro''' is the starting configuration file for the temperature equilibration.

It is the output of the energy minimization step.

|-
|| Cursor on the -r flag.
|| The r flag is used only when position restraint is used in the '''mdp''' file.

Go through the additional materials section to know more.

|-
|| Cursor on '''nvt.tpr'''.
|| The '''tpr''' file is the output file from this step.

|-
|| Cursor on the message.
|| While creating the file, few messages are seen on the '''terminal'''.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter '''ls''' on the '''terminal '''to list the files.

Notice the output '''nvt.tpr''' that is created.

|-
||
|| As done in the energy minimization step, we will enter the next commands.

|-
|| Type, '''gmx mdrun -v -deffnm nvt''' and press '''Enter'''.
|| Enter the command as seen to perform the temperature equilibration.

|-
|| Show the output on the '''terminal'''.
|| This time, the '''v flag''' shows only a few details.

The number of steps and time needed to complete are seen.

|-
|| Show the time taken for the process.
|| Process will stop when it reaches 50000 steps.

|-
|| '''Slide Number 8'''

'''Computation Time'''
|| * Having more steps in MD takes longer time.
* Use a computing facility to run these processes.
* Take care not to overheat or burn your computer.

|-
|| Press '''Ctrl+C'''.
|| You may run this process later on, if there is a time constraint right now.

To abort the process, press '''Control''' and '''C''' keys together once.

In a few minutes '''Gromacs''' stops the process.

|-
||
|| You may also pause the tutorial and allow the process to complete.

|-
|| Show files in the file manager.
|| Notice that several files with '''nvt''' prefix are generated in the working directory.

This step creates an additional new file format, the '''.cpt''' file.

|-
|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

|-
||
|| Delete the files from this aborted process.

|-
|| Show file deletion.
|| If you have completed the process, do not delete the files.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| An additional file '''gro''' will be created at the completion of the process.

Copy the '''nvt''' files provided for analysis to continue further.

|-
|| In the terminal Press '''Ctrl+L'''.
|| There are four files to be deleted and five files to be copied.

|-
| " | Type, '''gmx energy -f nvt.edr -o temperature.xvg''' and press '''Enter'''.
|| Using the '''energy''' command, let’s extract data from the '''nvt.edr''' file.

The prompt asks the user to select the parameters which are desired.

|-
|| Show the selection for parameters.

Type '''16'''.
|| Type '''16''' to choose the temperature of the system.

|-
|| Press '''Enter'''.
|| This number may be different for you.

|-
|| Show file in the '''file manager'''.
|| Let’s plot the temperature variation to check if the temperature is stabilized.

|-
|| Type, '''xmgrace temperature.xvg''' and press '''Enter'''.
|| '''Linux''' users can enter the command '''xmgrace space temperature.xvg''' in the terminal.

|-
|| Show opening the '''temperature.xvg''' file.
|| '''Windows''' users may open '''Qtgrace''', drag and drop the file on the graphics window.

|-
|| Cursor on the graph.
|| Notice that, the temperature fluctuates around 300 K.

Velocity variation in the system is given by '''Maxwell-Boltzmann'''
distribution.

|-
||
|| Particle collision due to '''Brownian''' motion fluctuates individual velocities.

However, the average temperature remains the same as set in the '''mdp''' file.

So we can proceed to the next step.

|-
|| Cursor on the graph.
|| If there are large fluctuations in temperature, please extend the run.

If you are plotting your own run data, these values will be different.

Each and every equilibration process will be unique and different.

|-
|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

|-
|| Type, '''gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr''' and press '''Enter'''.
|| Next, enter the command as seen here.

The output file '''nvt.gro''' from the previous step, is the input file in this step.

Here, files required to run the pressure equilibrium process is created.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command as seen to notice the '''npt.tpr''' file that is created.
|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity in the video.

|-
|| Type,

'''gmx mdrun -v -deffnm npt''' and press '''Enter'''.
|| Again, follow the usual commands and procedure for this step as seen here.

Enter the '''mdrun''' command as seen to start the pressure equilibration process.

|-
|| Press '''Ctrl+C''' to abort the process.
|| Yet again, allow the process to complete if you have time.

Else, abort the process and use the output files provided with this tutorial.

|-
|| Type '''ls''' and press '''Enter'''.
|| Enter the command, '''ls '''to notice the output files that are created.

|-
|| Show the provided nvt prefix files.

Show files copied in the working directory.
|| Else delete the files created from this aborted process.

If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional '''gro '''file will be created at the completion of the process.

|-
|| Cursor on '''npt.gro'''.
|| '''npt.gro''' is the output system from all the prior processes.

|-
|| Go back to the '''terminal'''.
|| Let’s extract and plot the pressure of the run from the '''npt.edr''' file.

Go back to the '''terminal'''.

|-
|| Type, '''gmx energy -f npt.edr -o pressure.xvg''' and press '''Enter'''.

Type '''18''' and press '''Enter''' twice.
|| Enter the energy command and choose 18 for pressure as seen here.

This number may be different for you.

|-
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.

Notice the fluctuations.

You may use the software of your choice for plotting.

|-
|| Cursor on the graph.
|| Sometimes the pressure values may show large fluctuations.

In some cases, they may not converge.

Hence '''density''' is a better estimate to check the system equilibrium.

Pause the video and go through the additional materials section to know more.

|-
|| Close '''Grace'''.
|| Let’s close '''Grace'''.

|-
|| '''Slide Number 9'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Ensemble properties and equilibration
* Run '''NVT''' and temperature equilibration
* Plotted the temperature fluctuation to check for equilibration
* '''NPT''' and pressure equilibration
* Plotted the pressure fluctuation

|-
|| '''Slide Number 10'''

'''Assignment'''
|| For assignment activity, please do the following.

* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
* Read publications of your choice using '''Gromacs'''.

|-
|| '''Slide Number 11'''

'''Assignment'''
||
* Open the '''nvt.gro''' and '''npt.gro''' files in '''VMD'''.
* Ascertain that, protein is not seen as two parts on two sides of the box.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.
|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.
|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Energy-Minimization/English

2021-12-14T07:21:34Z

Ranipv076: Created page with " {| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Energy Minimization'''. |- | | '''S..."

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Energy Minimization'''.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn about,

* Unfavorable interactions in the '''Gromacs''' generated file
* Commands to set up energy minimization
* '''mdrun''' and '''verbose''' option
* About '''edr''' file

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| | * Parameters for energy minimization
* The '''Energy''' command
* Create a file containing potentials in '''xvg''' format
* Plot and check the output file with '''Grace'''

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs v2021.2'''
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3
* '''Grace''' v5.1.25
* '''QtGrace''' v0.2.6 fork for '''Windows'''

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial,
* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided input files to the '''firstmd''' directory.
| | Several files are provided with this tutorial.

Copy the provided '''mdp''' file to the working directory.

|-
| | '''Ubuntu 20.04 LTS app''' ('''Windows''') or '''terminal''' ('''Linux''').
| | Open a '''terminal'''.

Windows users may open the '''Ubuntu''' 20.04 '''app'''.

|-
| | Type, '''cd Documents/firstmd''' and press '''Enter'''.
| | Change path to the '''firstmd''' directory, where the files are saved.

|-
| | Type, '''vmd ions-added.gro''' .
| | Let’s open the '''.gro''' file with the ions added, in '''vmd'''.

|-
| | VMD opens.
| | Windows users must first open '''VMD'''.

Then open the '''gro''' file in '''VMD'''.

|-
| | Point to the '''VMD''' Main window.

Click on '''Graphics, Representations'''.
| | We cannot see the ions clearly, among the large number of water molecules.

Hence, let’s change the display.

In the '''VMD Main''' window click on '''Graphics, Representations'''.

|-
| | Point to the window.
| | '''Graphical Representations''' window opens.
|-
| | Point to the''' Coloring Method.'''

Select '''Name''' in '''Coloring Method'''.
| | Select '''Name''' in '''Coloring Method'''.

|-
| | Type '''protein''' for '''Selected Atoms'''.

Press '''Enter''' and show protein in the graphics window.
| | Type '''protein''' for '''Selected Atoms''' and press '''Enter'''.

Now, only the protein is visible.

|-
| | Click on '''Create rep''' and select the newly created display.
| | Then click on '''Create Rep''' to create a new display.

Select the new display.

|-
| | For '''selected atoms''' type '''name CL''' and press '''Enter'''.
| | For '''selected atoms''' enter '''name space CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.
| | For '''Drawing method''', choose '''beads'''.

Notice the 8 chloride ions added randomly in the box.

|-
| | Type, '''pbc box''' in the '''vmd terminal prompt'''.
| | Let’s also display the box with the '''pbc box''' command in the '''vmd terminal'''.

Now the box is also displayed.

|-
| | Show '''VMD graphical window'''.
| | Adding several molecules and ions may create unfavourable atomic interactions.

|-
| |
| | Hence the input structure file of the system needs to be energy minimized.

This is a precursor procedure, before starting the '''MD''' simulation.

|-
| | Close '''VMD'''.
| | Let’s close '''VMD'''.

|-
| | Show files in file manager for '''firstmd''' directory.

'''em.mdp''' in a text editor.
| | Open the provided '''em.mdp''' file in a text editor and look at the parameters.

|-
| | Cursor on method '''integrator''' and '''nssteps'''.
| | Notice that, energy minimization uses '''steepest descent''' method.

One '''ps''' time duration is selected since minimization is for a short
timescale.

|-
| | Cursor over '''nstxout''' and '''nstlist'''.
| | The neighbor list is updated every 20 steps.

Every 10 steps the coordinates are written to a file.

|-
| | Cursor over '''pbc'''.
| | '''Pbc''' shows that, the periodic boundary condition is on.

Beginner may visualize '''pbc''' as follows.

If a molecule or atom diffuses out of the box, it will be added back to the box.

|-
| |
| | Learner may pause the video and explore the parameters further.

|-
| | Close the '''mdp''' file and go to the '''terminal'''.
| | Detailed information can be accessed from '''Gromacs''' documentation.

Close the '''mdp''' file and go to the '''terminal''' to start energy minimization.

|-
| | Type, '''gmx energy -f em.edr -o energy.xvg''' and press '''Enter'''.
| | Enter the '''grompp''' command as seen here.

'''em.mdp''' provides the parameters for the energy minimization.
|-
| | Cursor on '''ions-added.gro'''.
| | Here, Input file here is the output '''gro''' file from the '''genion''' command.

|-
| | cursor on '''em.tpr'''.
| | The '''tpr''' file is the output file from this step.

|-
| | Cursor on the interactions message.
| | The number of interactions the program will consider is shown here.

|-
| | Cursor on the molecule and atom details.
| | The protein atoms, number of solvent molecules and ions are also listed.

|-
| | Press '''Ctrl+L''' and press '''Enter'''.
| | I will clear the screen for clarity.

|-
| | Type '''ls''' and press '''Enter'''.
| | Enter '''ls''' on the terminal to list the files.

Notice the output files created.

|-
| | Type,

'''gmx mdrun -v -deffnm em''' and press '''Enter'''.
| | Next, enter the command as seen to perform the actual energy minimization.

The '''deffnm''' flag tells gromacs to use the em prefix for the generated files.

|-
| | Show the output on the '''terminal'''.
| | '''Hyphen v''' flag means the output is '''verbose'''.

'''Gromacs''' will display the output details in real time on the '''terminal'''.

|-
| | Cursor on the '''terminal'''.
| | Without this flag, user will not see the steps or the details displayed.

This process will take some time to complete, depending on your computer.

|-
| |
| | Notice the step number, energy and size parameters for each iteration.

Energy minimization will stop when it reaches below 500 KJ/mol.

|-
| | Show screenshot of em.mdp file contents.
| | It is set in the '''mdp''' file.

|-
| |
| | Learner may study the '''mdp''' file to know more about the parameters.

|-
| | Press '''Ctrl+C'''.
| | If there is time constraint right now, you may abort the process.

For this press the '''Control''' and '''C''' keys together.

|-
| | Show the files''' em.edr, em.trr, em.log'''.
| | You may also pause the tutorial and allow the process to complete.

Else delete the files from this aborted process.

If aborting the process, use the provided files for further analysis.

|-
| | Show the file '''em.gro''' which is to be copied.
| | If you have completed the process, do not delete the files.

Copy the files provided for analysis to continue further.

An additional gro files will be created at the completion of the process.

|-
| | Go to file manager.
| | These files are provided for you as samples with this tutorial.

Please copy them to the working directory.

They have extensions, '''edr''', '''log''' and '''trr'''.

|-
| | show the four files.
| | They have extensions, '''edr''', '''log''', '''trr''' and '''tpr'''.

|-
| | Cursor on '''trr''' and '''edr''' files.
| | The '''trr''' are trajectory files.

'''edr''' file contains details such as energies, temperature and so on.

|-
| | Type, '''gmx energy -f em.edr -o potential.xvg''' and press '''Enter'''.
| | Using the '''energy''' command, let’s extract data from the '''em.edr''' file.

The hyphen '''o''' flag is the output filename.

|-
| | Show the selection for parameters.

Type '''11'''.
| | The prompt asks user to select the parameters which are desired.

I will type '''11''' to choose '''potential''' for selecting the energy of the system.

This selects the energy of the system.

|-
| | Press '''Enter''' twice.
| | This number may be different for you.

Press '''Enter''' to exit.

|-
| | Show '''potential.xvg''' file in the '''file manager'''.
| | '''Potential.xvg''' file gets created.

This file can be opened by the G'''race''' program.

|-
| | Type, '''xmgrace potential.xvg''' and press '''Enter'''.

Point to the plot window.
| | I have already installed '''Grace''' on the computer.

'''Linux''' users can enter the command, '''xmgrace space potential.xvg''' in the '''terminal'''.

'''Grace''' window opens with the plot.

|-
| | Cursor on the graph.
| | Notice the higher potential at the starting point.

The energy decays smoothly and we completed about 1400 steps.

You may choose to learn the use of these software for ease of data analysis.

|-
| | Close '''Grace '''window.
| | Let’s close '''grace '''window.

|-
| | Show '''Qtgrace directory''' and open '''Qtgrace'''.

Show opening the '''potential.xvg''' file.
| | '''Windows''' users may install '''Qtgrace''' fork for analysis.

Open '''Qtgrace''', drag and drop the '''xvg''' file icon on the graph window to open it.

|-
| | Resize graph to fit into recording window.
| | Importing the '''xvg''' file through the menu options may show errors.

If you are plotting your own data, these values will be different.

Every '''MD''' run or '''minimization''' will have it’s own unique '''trajectory'''.

|-
| |
| | Users may also use '''gnuplot''' for data analysis if desired.

|-
| | Show spoken tutorial website series for '''Grace''' and '''Gnuplot'''.
| | Spoken tutorial website has tutorials on both software for your convenience.

'''gnuplot''' is also suited to create '''3D''' or surface plots.

|-
| |
| | Spreadsheet editors such as Libreoffice Calc, Excel can also be utilized.

|-
| | Screenshot of the '''energy''' command options to export to '''xvg''' file.
| | You may pause this video, to create and plot more parameter outputs.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we learned about,

* Unfavorable interactions in the in the '''Gromacs''' generated file
* Commands to set up energy minimization
* About '''mdrun''' and '''verbose''' option
* About .'''edr''' file

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Parameters for energy minimization
* About '''energy''' command
* Created a file containing potentials in '''xvg''' format
* Plotted the '''xvg''' file with '''Grace'''

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

* Extract few more parameters from the '''.edr''' file with the '''energy''' command.
* Create and view the graphs with a plotting program of your choice.

|-
| | '''Slide Number 10'''

'''Assignment'''
| |
* Open the '''em.gro''' file in '''VMD''' or another program of your choice.
* Ascertain the protein molecule is seen as one unit in the box.

|-
| | '''Slide Number 11'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 12'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 13'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 14'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-12-09T01:47:03Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open the '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files, with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up, to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| Reference for the publication is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.gro''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created '''solvated.gro''' file in a text editor.

Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the net charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will create a '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file contains parameters required to assemble the system for '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

This file defines several parameters for the '''MD''' run.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type, '''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges.

|-
|| Open the file manager.
|| Open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

I will choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

They are replaced by the ions.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files containing coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,
* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-12-08T17:21:05Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open the '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files, with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up, to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| Reference for the publication is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.gro''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created '''solvated.gro''' file in a text editor.

Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the net charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will create an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file contains parameters required to assemble the system for '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

This file defines several parameters for the '''MD''' run.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

I will choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

They are replaced by the ions.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files containing coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,
* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-12-08T17:14:34Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open the '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files, with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up, to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| Reference for the publication is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created '''solvated.gro''' file in a text editor.

Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file contains parameters required to assemble the system for '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

This file defines several parameters for the '''MD''' run.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

I will choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

They are replaced by the ions.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files containing coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,
* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T09:26:39Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up, to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| Reference for the publication is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created '''solvated.gro''' file in a text editor.

Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file contains parameters required to assemble the system for '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

This file defines several parameters for the '''MD''' run.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

I will choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

They are replaced by the ions.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files containing coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,
* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T09:04:23Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up, to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| Reference for the publication is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created '''solvated.gro''' file in a text editor.

Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file contains parameters required to assemble the system for '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

This file defines several parameters for the '''MD''' run.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T07:55:17Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up, to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| Reference for the publication is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created '''solvated.gro''' file in a text editor.

Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T07:45:01Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

This command adds the water molecules in the box with '''lysozyme.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the input file.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Then specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| A reference paper is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created file '''solvated.gro''' file in a text editor.
Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T06:18:44Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water for aqueous medium or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This file has 216 water molecules.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may also do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| Cursor on '''VMD'''.
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the '''solvate''' command as seen here.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the position and aligned input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Then specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| A reference paper is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created file '''solvated.gro''' file in a text editor.
Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T06:09:04Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This particular file has 216 water molecules in the box.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| '''Slide Number 7'''

'''FIle Paths for Windows Users'''
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the command as seen here.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the position and aligned input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Then specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| A reference paper is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created file '''solvated.gro''' file in a text editor.
Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T06:03:47Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This particular file has 216 water molecules in the box.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| '''Slide Number 7'''

'''FIle Paths for Windows Users'''
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the command as seen here.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the position and aligned input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Then specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| A reference paper is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created file '''solvated.gro''' file in a text editor.
Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-10T06:00:23Z

Ranipv076:

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * About '''mdp''' file
* Generate '''tpr''' file with the '''grompp''' command and
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This particular file has 216 water molecules in the box.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| '''Slide Number 7'''

'''FIle Paths for Windows Users'''
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the command as seen here.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the position and aligned input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Then specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| A reference paper is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created file '''solvated.gro''' file in a text editor.
Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C3/Solvate-and-Grompp-Commands/English

2021-11-08T18:36:38Z

Ranipv076: Created page with "{| border=1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the tutorial on '''Solvate and grompp commands'''. |- || '''S..."

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''Solvate and grompp commands'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,

* Solvent input files with coordinates
* Add solvent molecules to the system with '''solvate''' command
* Open the '''solvated.gro''' file in '''VMD'''

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * About '''mdp''' file
* and Generate '''tpr''' file with the '''grompp''' command
* Add ions to the system with the '''genion''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Gromacs''' v2021.2
* '''Firefox''' web browser v92
* '''Gedit''' v3.36
* '''VMD''' 1.9.3

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
||
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open '''File manager'''.

Show files in the '''firstmd''' working directory.
|| Open '''File manager''' .

Copy the necessary input files to the working directory.

|-
|| Cursor on the page.
|| Let’s learn about adding solvent molecules in the box with the protein.

The input file for adding solvent is the output file from the '''editconf''' command.

|-
|| Open '''File manager''' and go to the extracted '''Gromacs''' tarball.
|| In the '''File manager''', go to the extracted directory of '''Gromacs''' tarball.

|-
|| Go to the '''Share''' directory, then to the '''top''' directory.
|| Go to the '''share''' directory in the downloaded '''Gromacs''' files.

Navigate to the '''top''' directory.

|-
|| Search for '''.gro''' files in the directory.

Show the files.
|| Search for file with '''.gro''' extension and notice few files in it.

Water and '''methanol''' solvent types are available in the downloaded files.

|-
|| Cursor on the water solvent files.
|| Notice files with water solvation in different types.

|-
|| Cursor on methanol solvent file.
|| '''Methanol''' file is provided as an example organic solvent system as seen here.

|-
||
|| Users may desire to add water or organic solvents.

|-
|| Open the '''tip4p.gro''' file in a text editor.
|| Let’s open the '''tip4p.gro''' file in a text editor.

|-
|| Cursor on the header and file.
|| Header line shows the number of water molecules, box size and temperature.
This particular file has 216 water molecules in the box.

Solvent file can be customized to user preference.

|-
|| Close '''tip4p.gro''' file.
|| Let’s close the text editor.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' '''app'''.

|-
|| Type, '''cd Documents/firstmd''' and press '''Enter'''.
|| I will change to the '''firstmd''' directory, where all the files are saved.

|-
|| Type, '''vmd box-added.gro''' and press '''Enter'''.
|| Linux users may do the following.

Enter '''vmd''' space '''box-added.gro''', to open the input file in '''VMD'''.

|-
|| '''Slide Number 7'''

'''FIle Paths for Windows Users'''
|| '''Windows''' users must open '''VMD''' through windows.

Locate the path of the '''box-added.gro''' file in your computer and open it.

|-
|| Show the graphics interface.
|| '''VMD''' opens with the aligned, centered molecule in the graphics interface.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
||
|| Let’s command add the water molecules inside the box around '''lysozyme'''.

|-
|| Close '''VMD'''.
|| Let’s close '''VMD'''.

|-
|| Type, '''gmx solvate -cp box-added.gro -cs tip4p.gro -p topol.top -o solvated.gro'''
|| Enter the command as seen here.

|-
|| Highlight '''-cp '''.
|| Here '''-cp''' flag denotes the position and aligned input file of the protein structure.

|-
|| Continue to type, '''-cs tip4p.gro''' .
|| The '''-cs''' flag is added before the solvent coordinate file.

Then '''Gromacs''' identifies it as the solvent file that is to be added to the box.

|-
|| Type '''-p topol.top -o solvated.gro '''.
|| We will also update the '''topology''' file.

Then specify the output filename with hyphen '''o''' flag.

|-
|| Press '''Enter''' and then scroll up.
|| Let’s execute the command, and scroll up to see the messages.

|-
|| Cursor on the output details.
|| The program gives a detailed output.

Notice that many water molecules are added in the file.

Amino acid residues of the protein come from the '''1AKI.pdb''' file.

|-
|| Highlight '''‘PLEASE READ AND CITE THE FOLLOWING REFERENCE’'''.
|| A reference paper is also seen with a message for users to read it.

Please read and understand it.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''vmd solvated.gro''' and press '''Enter'''.
|| Enter '''vmd''' space '''solvated.pdb''', to open the newly created file in '''VMD'''.

|-
|| Show the graphics interface.
|| Notice the protein and water molecules in the graphics window of '''VMD'''.

|-
|| Type '''pbc box''' in the '''terminal'''.
|| Enter the command '''pbc''' space '''box''' in the '''VMD''' command prompt.

This will show the box in the graphical interface.

|-
|| Cursor around the box.
|| The water molecules are positioned inside the box, around the protein.

The shape and dimensions of this box was defined in the '''editconf''' command.

|-
|| Cursor outside box.
|| Outside the box is vacuum.

There are no solvent molecules present outside.

|-
||
|| Motion of the protein inside this box is simulated for a duration in '''MD'''.

|-
|| Close '''VMD'''.
|| Hence, the input structure file of the system needs to be energy minimized.

Let’s close '''VMD'''.

|-
|| Show solvated '''.gro''' in the File Manager.
|| Open the newly created file '''solvated.gro''' file in a text editor.
Pause this video, scroll down the file, and notice the added water molecules.

|-
|| Cursor on the file.
|| The '''tip4p.gro''' file for solvent that we added had only 216 water molecules.

However, more are present in this file.

|-
|| Cursor on the number of water molecules.
|| When the box size increases, the number of water molecules will also increase.

|-
||
|| Next, we will add ions to the system to neutralize the let charge.

|-
|| Close the '''topology.top''' file.
|| Let’s close the topology file.

|-
|| Cursor on the '''File manager'''.
|| '''Gromacs''' will replace few solvent molecules with ions of choice.
|-
||
|| For this purpose, we will use an '''mdp''' file.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0.4/online/mdp.html https://manual.gromacs.org/archive/5.0.4/online/mdp.html] '''.
|| Open a web browser and go to this site.

'''Mdp''' stands for '''molecular dynamic parameters'''.

|-
|| Cursor on the web page.
|| Example '''mdp''' files are available on the '''Gromacs''' website.

'''Gromacs''' also uses a '''mdp''' file, to assemble the system configuration.

This file defines several parameters for the '''MD''' run.

Parameters such as time interval, number of steps or temperature are given.

|-
|| Go to the '''terminal'''.
|| Let’s go to the '''terminal'''.

|-
|| Type,

'''gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o input1.tpr -maxwarn 1'''

and press '''Enter'''.
|| Enter the '''grompp''' command as seen here to generate the input file.

'''Grompp''' is the '''preprocessor''' command to generate the structure file.

|-
|| Highlight '''grompp'''.
|| We will use the '''mdp''' file provided with this tutorial with fewer parameters.

|-
|| Highlight input and '''topology''' file.
|| Input file is the solvated molecule in the box.

The '''.top''' is the '''topology''' file.

|-
|| Highlight '''-maxwarn 1'''.
|| There could be a charge difference between the system and topology file.

To ignore it in this step, we will add the '''maxwarn''' flag and set it to 1.

Users must be careful when using this flag.

|-
|| Highlight '''input1.tpr'''.
|| The '''tpr''' file is the output.

This is not a text file like earlier outputs.

|-
||
|| To know what is in the file, you need to convert it to a user readable format.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen for clarity.
|-
|| Type,

'''gmx dump -s input1.tpr''' and press '''Enter'''.
| " | Let’s use the '''dump''' command as seen here to make it readable.

|-
|| Scroll up the file.
| " | Scroll up and notice the file and the many details added to the structure file.

|-
|| Show the '''dump''' file.
|| Let’s add ions to the system to balance charges in the system.

|-
|| Open the file manager.
|| Let’s open the file manager.

First find the charge on the system from the topology file.

|-
|| Highlight the file '''topol.top.1#'''
|| We will use the topology file generated by the '''pdb2gmx''' command.

|-
||
|| '''Gromacs''' backs up the '''topology''' files with the hash suffix as seen here.

|-
|| Highlight the line in the file, which gives the command which created it.
|| I will open this file in a text editor.

This file was created by the '''pdb2gmx''' command.

|-
|| Scroll through the file.
|| Scroll down to find the total charge which is represented by the '''qtot''' line.

|-
|| Go to the last line of '''qtot'''.
|| Go to the last line of '''qtot''', which gives the total charge in the system.

|-
|| Highlight '''8'''.
|| Here, it is 8.

Hence, to create a neutral system, we need to add 8 negative charges.

|-
|| Close the '''topology''' file.
|| Let’s close the '''topology''' file.

|-
|| Press '''Ctrl+L'''.
|| I will clear the screen.

|-
|| Type, '''gmx genion -s input1.tpr -o input2-ions.gro -p topol.top -pname NA -nname CL -nn 8 '''.
|| The '''genion''' command adds ions to the system.

'''pname''' is for positive ion and NA stand for sodium ion.
'''nname''' is for negative ion, which is chloride ions here.

The '''nn''' flag tells '''Gromacs''' how many '''chloride''' ions are to be added to the system.

|-
|| Press the '''Enter''' key'''.'''
|| The '''nn 8''' flag can be replaced by '''neutral''' flag to create a neutral system.

|-
|| Highlight the options for replacing.
|| The user is prompted to choose which atoms are to be replaced from the box.

|-
|| Type '''13''' for solvent.
|| We don’t want to replace the atoms of the protein with ions.

Choose '''13''' to replace solvent molecules for ions.

|-
|| Scroll up and show the changes.
|| Notice that, the number of water molecules in the box have decreased.

|-
|| '''Slide Number 7'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* Solvent input files with coordinates
* Added solvent molecules with '''solvate''' command
* About '''mdp''' file

|-
|| '''Slide Number 8'''

'''Summary'''
|| * Opened the solvated '''gro''' file in '''VMD'''
* Generated a '''tpr''' file with the '''grompp''' command
* About '''dump''' command
* Added ions with '''genion''' command

|-
|| '''Slide Number 9'''

'''Assignment'''
|| For assignment activity, please do the following.

* Use a '''PDB ID''' of another protein of your choice.
* Practice the commands learnt in this tutorial.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| From the '''Gromacs''' manual ,* Read on the following file extensions.
** top, gro , mdp , tpr , itr
* Create a table to keep track of which file gets generated in which step.

|-
|| '''Slide Number 11'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 13'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-26T11:50:38Z

Ranipv076:

{|border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About selecting a force field
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
||
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to '''Documents''' using the '''cd''' command as seen.

|-
|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first.
Hence, type '''mkdir''' space '''Documents''' before changing path.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change directory to the newly created '''firstmd''' directory.

|-
|| '''Slide Number 7'''

'''File path for Windows Users'''
||
* '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager'''.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' input file to this directory.

For Windows users this path is likely to be in C drive and in the user system folder.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a stable, well studied model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for us.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate the input files for '''MD'''.

|-
|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax.
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several force fields are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details of publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

I want to select '''AMBER99'''.

To select '''AMBER''', type '''4''' and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| '''Gromacs''' returns the '''force field''' as '''amber99.ff''' that will be used .

By convention, '''.ff''' extension denotes '''force field '''files.

The path of the file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore the solvent addition.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''top''' is the '''topology''' file and '''.itp''' is '''include topology''' file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' for clarity in the video.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like before '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1 nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''gro''' file, with box size and file name.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning with the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,
* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a '''force field'''
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

|-
|| '''Slide Number'''

'''Summary 9'''
||
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
||
* Go to the website seen below.
* Choose a tutorial of your choice and read it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-26T11:39:02Z

Ranipv076:

{|border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About selecting a force field
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
||
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to '''Documents''' using the '''cd''' command as seen.

|-
|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first.
Hence, type '''mkdir''' space '''Documents''' before changing path.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change directory to the newly created '''firstmd''' directory.

|-
|| '''Slide Number 7'''

'''File path for Windows Users'''
||
* '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager'''.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' input file to this directory.

For Windows users this path is likely to be in C drive and in the user system folder.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a well studied, stable and model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax.
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several force fieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER99'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files.

The path of the file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore more on the solvent addition.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''.gro''' file, with box size and file name.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,
* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

|-
|| '''Slide Number'''

'''Summary 9'''
||
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
||
* Go to the website seen below.
* Choose a tutorial of your choice and read it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-24T16:59:09Z

Ranipv076:

{|border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About selecting a force field
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' 3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
||
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to Documents using the cd''' command as seen.

|-
|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first.
Hence, type '''mkdir Documents''' before changing path with '''cd''' command.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change path to the newly created '''firstmd''' directory.

|-
|| '''Slide Number 7'''

'''File path for Windows Users'''
||
* '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager'''.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' file input file to this directory.

For Windows users this path is likely to be in C drive.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a well studied, stable and model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax.
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several force fieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER99'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files.

The path of the file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore more on the solvent addition.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''.gro''' file, with box size and file name.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,
* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

|-
|| '''Slide Number'''

'''Summary 9'''
||
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
||
* Go to the website seen below.
* Choose a tutorial of your choice and read it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-24T16:58:10Z

Ranipv076:

{|border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* About selecting a force field
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' 3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
||
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to Documents using the cd''' command as seen.

|-
|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first.
Hence, type '''mkdir Documents''' before changing path with '''cd''' command.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change path to the newly created '''firstmd''' directory.

|-
|| '''Slide Number 7'''

'''FIle path for Windows Users'''
|| * '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager'''.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' file input file to this directory.

For Windows users this path is likely to be in C drive.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a well studied, stable and model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax.
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several forcefieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER99'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files.

The path of the file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore more on the solvent addition.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''.gro''' file, with box size and file name.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,
* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

|-
|| '''Slide Number'''

'''Summary 9'''
||
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
|| * Go to the website seen below.
* Choose a tutorial of your choice and read it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-24T16:56:36Z

Ranipv076:

{|border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * About selecting a force field
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' 3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
||
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to Documents using the cd''' command as seen.

|-
|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first.
Hence, type '''mkdir Documents''' before changing path with '''cd''' command.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change path to the newly created '''firstmd''' directory.

|-
|| '''Slide Number 7'''

'''FIle path for Windows Users'''
|| * '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager'''.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' file input file to this directory.

For Windows users this path is likely to be in C drive.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a well studied, stable and model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax.
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several forcefieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER99'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files.

The path of the file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore more on the solvent addition.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''.gro''' file, with box size and file name.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,

* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

|-
|| '''Slide Number'''

'''Summary 9'''
||
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
|| * Go to the website seen below.
* Choose a tutorial of your choice and read it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-24T16:56:21Z

Ranipv076:

{border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting '''pdb''' file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * About selecting a force field
* Specifiy the size and shape of bounding box for MD
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' 3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''Code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser.
Go to the '''Gromacs''' manual link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
||
|| Let’s consolidate all our input files into one folder.
From now on, I will not mention this separately.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''cd Documents''' and press '''Enter'''.
|| '''Linux''' users can change directory to Documents using the cd''' command as seen.

|-
|| Windows users may skip this step and remain in '''home''' directory.
|| Windows users must create this directory first.
Hence, type '''mkdir Documents''' before changing path with '''cd''' command.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| I will create a new directory and name it '''firstmd'''.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change path to the newly created '''firstmd''' directory.

|-
|| '''Slide Number 7'''

'''FIle path for Windows Users'''
|| * '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved here.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager'''.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the '''1AKI.pdb''' file input file to this directory.

For Windows users this path is likely to be in C drive.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Then, open the '''pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In most files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is a well studied, stable and model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Go to the '''terminal'''.
|| GO back to the '''terminal'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| Enter the commands as seen and retain the syntax.
All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several forcefieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER99'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files.

The path of the file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Notice that only an aqueous environment is present in the list.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
|| Show output and total charge of the system.
|| In the output notice the total charge on the system listed.
Learner is encouraged to pause the video and explore more on the solvent addition.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file in a text editor.

Notice that, this command has also added hydrogens.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like '''pdb2gmx''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which is cubic.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

Cubic and hexagonal shapes are popularly used for the bounding box.

This generates another input '''.gro''' file, with box size and file name.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,

* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files
* About '''editconf''' command

|-
|| '''Slide Number'''

'''Summary 9'''
||
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
|| * Go to the website seen below.
* Choose a tutorial of your choice and read it.

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/Creating-Input-Files/English

2021-10-21T14:00:24Z

Ranipv076: Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the spoken tutorial on '''Creating Input Files'''. |- || '''..."

{| border=1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting pdb file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| * About force field and selecting a force field
* Generate the '''topology''' file
* '''editconf''' command

|-
|| '''Slide Number 4'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' 3.36
* '''Gromacs''' v2021.2

|-
|| '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 6'''

'''Code Files'''
|| * Files used in this tutorial are provided in the '''code files''' link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser and go to the '''Gromacs''' link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| Type '''mkdir space firstmd''' to create a new directory.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change path to the newly created '''firstmd''' directory with the '''cd''' command.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager''' and go to the '''firstmd''' directory.

|-
||
|| Let’s consolidate all our input files here.

From now on, I will not mention this separately.

|-
|| '''Slide Number 7'''

'''FIle path for Windows Users'''
|| * '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved to here.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the provided '''1AKI.pdb''' input file to this directory.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Open the '''1AKI.pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In many files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is well studied, stable and a model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

Enter the commands as seen and retain the syntax.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file input file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several forcefieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the number for the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER94'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files and the path of file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
||
|| Sometimes, users desire for different solvent system to be added.

If so, create a '''topology''' file and add it to the library.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file that gets created in a text editor.

Notice that, this command has also added hydrogens to the file.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5th and 6th columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the '''firstmd.gro''' file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like the '''editconf''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the

center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| If using '''lysozyme''', the max length for '''lysozyme''' can be of the order of 90 A.

So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which I will enter to be of cubic shape.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

This generates another input '''.gro''' file, with box size and sets file names.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

Close the text editor window.

|-
|| '''Slide Number'''

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,

* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files

|-
|| '''Slide Number'''

'''Summary 9'''
||
* About '''editconf''' command
* Define the size of a bounding box
* Set the position of the molecule in the box

|-
|| '''Slide Number'''

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

|-
|| '''Slide Number'''

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
|| * Go to the website seen below.
* Choose a tutorial of your choice and read it

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''
|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/PDB-File-Format-and-Website/English

2021-10-21T13:18:33Z

Ranipv076:

{| border =1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''PDB File Format and Website'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn,

* About PDB file format for molecular structure
* Protein Data Bank ('''PDB''') website
* Download a '''pdb''' file from '''PDB''' website
* About '''FASTA''' file format

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36.2
* A working internet connection to access the '''PDB''' website

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''File from downloaded tarball'''
|| Files used in this tutorial, can be found in the,
* Downloaded and extracted tarball directory used for '''Gromacs''' installation

|-
|| Open the File manager.
|| Let’s open the '''File manager'''.

Go to the downloaded and extracted tarball directory for '''Gromacs''' installation.

|-
|| Cursor on the files of the extracted '''Gromacs''' directory.

Go to '''src''' directory.
|| Few test '''PDB''' files are given for testing purposes with '''Gromacs''' installation.

They can be found in the '''src''' directory of the extracted tarball of '''Gromacs'''.

|-
|| Navigate to '''testutils''' directory and then to '''simulationdatabase'''.
|| Now, navigate to '''testutils''' directory and then to '''simulationdatabase'''.

|-
|| Scroll down and cursor on the '''lysozyme.pdf''' file.
|| Scroll down and notice the '''lysozyme.pdb''' file.

|-
|| Open '''lysozyme.pdb''' in a text editor.
|| Let’s open this file in a text editor.

This file is in '''PDB '''file format, and the structure of truncated '''lysozyme'''.

|-
|| Cursor on the file.
|| The file gives the coordinates in '''xyz''' axes of each atom in a molecule.

It is in the '''PDB''' format defined by '''IUPAC''' convention.

|-
|| '''Slide Number 6'''

'''Protein Data Bank'''

[https://www.rcsb.org/ https://www.rcsb.org/] '''
|| * '''Protein data bank''' is a repository of 3D structural data of biomolecules
* The website link is shown here.
* The structures are determined by '''X-ray''' diffraction, '''NMR''', & '''electron microscopy'''

|-
|| '''Slide Number 7'''

'''Protein Data Bank'''
|| Atomic resolution structures for
* Proteins, DNA and RNA
* Carbohydrates and lipids
* Several ligand molecules
are available here

|-
|| Cursor on the first 3 lines.
|| The first few lines on the top are comments, giving details about the file.

|-
|| Cursor on '''MODEL'''.
|| The '''MODEL''' indicates the first set of coordinates which is listed below it.

This happens when more than a single coordinate set is selected to represent the molecule.

|-
|| Cursor on page.
|| Learner can refer to structures determined by '''NMR''' method, to know more.

In '''NMR''' an ensemble of structure is selected to represent the molecule.

|-
|| Cursor on the '''ATOM''' lines.
|| Notice the several columns below '''MODEL'''.

Each row gives details of each '''atom''' in the biomolecule.

|-
|| Cursor on the first and second column.
|| The first column shows, it is for the atom.

The second column incrementally counts each atom in the molecule.

|-
|| Cursor on the third and fourth column.
|| Third column gives the atom name.

The next column shows the amino acid residue.

|-
|| Cursor on 5th and 6th column.
|| Fifth column is the subunit number.

Sixth column is the residue position number of the atom in the biomolecule.

|-
|| Cursor on 7, 8, and 9 columns.
|| The next three columns are the '''x, y''', and '''z''' coordinates.

They are the position of the atom in the biomolecule in 3 dimensional space.

|-
|| Cursor on the 10th column.
|| The 10th column is the occupancy of the atom at that position.

|-
|| Cursor on 11th and 12th column.
|| Then notice the '''R''' factor.

The last column lists the element that occupies the position.

|-
|| Scroll down and show '''TER''' line in the file.
|| Scroll to the end of the file and notice the '''TER''' written here.

This denotes the end of the molecular model and the molecule.

|-
|| Cursor on residue number 10.
|| Notice that, the data is truncated at the 10th residue in this document.

This file is for demonstration purpose only.

|-
|| Cursor on the interface and close the text editor.
|| All residues for '''1AKI''' which is the '''lysozyme''' entry are not present here.

Lysozyme, or full length deposition of '''1AKI''' has 129 amino acid residues.

Let’s consult the '''PDB''' site to know more.

Let’s close the text editor.

|-
|| Open web browser and go to [https://www.rcsb.org/ https://www.rcsb.org/] .
|| Next, open a web browser.

Go to the '''PDB''' website as seen here.

Let’s learn to search and download coordinates from the '''PDB''' website.

|-
|| Enter '''lysozyme''' in the search form on top and press '''Enter'''.
|| In the search form on the top, let’s enter '''lysozyme'''.

|-
|| Scroll down.
|| Scroll down the page and notice the several search results for '''lysozyme'''.

Each molecular structure that is deposited in the '''PDB''' has a unique ID.

|-
|| Scroll up and enter '''1AKI''' in the search form.
|| Now, go to the top of the page.

Click on '''Search, Basic Search'''.

Let’s search for the structure deposition ID '''1AKI'''.

|-
|| Show details of '''1AKI'''.
|| Now the structure deposition details of this protein ID, appears.
The page opens in the '''Structure Summary''' tab.

|-
|| Cursor on the page and scroll down.
|| Scroll down and notice the detailed information on this structure.

It is that of egg white '''lysozyme'''.

|-
|| Cursor on '''X-ray diffraction'''.
|| Notice that it is determined by '''X-ray diffraction''' method.

|-
|| Click on '''3D View''' tab.
Scroll to the top of the page.
|| Scroll to the top of the page and click on the '''3D View''' tab.

Scroll down the page.

An interactive window is seen on the left with the protein structure.

|-
|| Click, hold and move mouse, show protein in rotated view.
|| Click, hold and move the mouse to rotate the protein in the window.

|-
|| Cursor on primary sequence and click on 2-3 residues.

Move cursor to the protein to show the highlighted position.
|| On the top of the screen, notice the protein primary sequence.

Click on any of the residue and notice it highlighted in the structure.

|-
|| Cursor on the protein structure.
|| Currently, the secondary structure of the protein is also visible.

|-
|| Cursor on red dot.
|| All the red dots are water molecules.

Users may pause this video and explore all the details given on this '''PDB''' ID.

|-
|| Scroll up the page.
|| Let’s scroll up the page and download the molecule structure coordinate file.

|-
|| Cursor on '''Display files''' and '''Download files'''.
|| Notice the '''Display files''' and '''Download files''' pulldown towards the top right.

|-
|| Click on the '''Display files'''.
|| Click on the '''Display files''' and notice the '''FASTA''' '''Sequence''' option.

|-
|| Click on '''FASTA'''.
|| Click on it.

|-
|| Cursor on the '''FASTA''' sequence tab.
|| A new tab opens with the '''primary''' sequence of the protein in single letter code.

The first line is the header giving the ID and details about the sequence.

|-
|| Close the '''FASTA''' tab.
|| I will close this tab.

|-
|| Click on the '''PDB format''' option.
|| Next click on the '''PDB format''' option in the '''Display files''' pulldown.

|-
|| Cursor on the new tab with the '''PDB''' file.
|| Again, a new tab opens with the '''PDB''' file.

|-
|| Cursor on the header lines.
|| The first several lines are headers which give details about the deposition.

|-
|| Cursor on details on top.
|| Notice the organism, name, authors, publication details and resolution.

|-
|| Scroll down the page.
|| Scroll down the page and notice more details.

Learner may pause this video and explore the PDB file in detail.

|-
|| Cursor on '''SSBOND'''.
|| Any disulfide bond present in the protein is also listed here.

|-
||
|| Often small molecule ligand or more chains are present in the system of study.

If so, their details will also be visible in the header.

|-
|| Cursor on the atomic coordinates.
|| The coordinates for each atom in the unit structure is listed below.

|-
|| Cursor on the atomic coordinates.
|| Notice that there are no hydrogens listed here.

This is because the x-ray diffraction method does not detect hydrogens.

|-
|| Curson on '''1AKI''' file opened in text editor.
|| The '''1AKI''' file, which we opened earlier, had hydrogen atoms added to the file.

The file also had a trimmed header.

Hydrogen atoms are added to the molecule afterwards as needed by the users.

|-
|| Scroll down.

Cursor at '''TER'''.
|| Now, scroll almost to the end of the page.

|-
|| Cursor on '''HETATM'''.

Point to the HOH atoms in the file.
|| Below '''TER''' tag, this there are many hetero atoms listed now.

They are water molecules that are present in the protein crystal.

|-
|| Show '''O''' element for '''HETATM'''.
|| Notice that, here too, hydrogens will not be observed.

|-
|| Show '''O''' element for '''HETATM'''.
|| Often, these water molecules are removed from the PDB file, before simulation.

|-
|| Close the '''PDB''' details tab.
|| Let’s close the '''PDB''' details tab.

|-
|| Click on the '''Download Files''' pulldown.
|| Now, click on the '''Download Files''' pulldown.

|-
|| Choose the '''PDB format'''.
|| Choose the '''PDB format'''.

A dialog box may or may not open prompting to save the file.

|-
|| Choose '''Save File''' and click on '''Ok'''.
|| If so, choose to save the file on the computer and click on '''Ok'''.

Allow the file download to complete.

|-
|| Cursor on the PDB web page.
|| Learner may pause this video and open the downloaded file in a text editor.

Notice that the file we viewed and downloaded are the same.

|-
|| Cursor on the PDB web page.
|| Open the '''PDB''' file in '''VMD''' or another molecular viewer.

Notice the structure displayed.

|-
|| '''Slide Number 8'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* The '''PDB''' file format
* The '''PDB''' website
* '''FASTA''' file format
* Header details in the '''PDB''' file
* Downloaded a '''pdb''' file

|-
|| '''Slide Number 9'''

'''Assignment '''
|| For assignment activity, please do the following.

* Go through the '''PDB''' website
* Familiarize with more details given for the PDB deposition.
* Go through the header details of the file that is downloaded.

|-
|| '''Slide Number 10'''

'''Assignment '''
|| Go through the given IDs from '''PDB''' website for enzyme '''DHFR''' and it’s complexes.

* '''2L28''' for '''apo enzyme''' and multiple '''conformer'''s
* '''1DIS''' for '''binary''' complex
* '''3DAT''' for '''ternary''' complex

|-
|| '''Slide Number 11'''

'''Assignment '''
||
* Notice the presence and absence of hydrogen atoms in the structure files
* Familiarize with
** Conformational changes in the enzyme
** Hydrogen bonding with ligands

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''

|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/PDB-File-Format-and-Website/English

2021-10-21T13:11:40Z

Ranipv076:

{| border =1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''PDB File Format and Website'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn,

* About PDB file format for molecular structure
* Protein Data Bank ('''PDB''') website
* Download a '''pdb''' file from '''PDB''' website
* About '''FASTA''' file format

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36.2
* A working internet connection to access the '''PDB''' website

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''File from downloaded tarball'''
|| Files used in this tutorial, can be found in the,
* Downloaded and extracted tarball directory used for '''Gromacs''' installation

|-
|| Open the File manager.
|| Let’s open the '''File manager'''.

Go to the downloaded and extracted tarball directory for '''Gromacs''' installation.

|-
|| Cursor on the files of the extracted '''Gromacs''' directory.

Go to '''src''' directory.
|| Few test '''PDB''' files are given for testing purposes with '''Gromacs''' installation.

They can be found in the '''src''' directory of the extracted tarball of '''Gromacs'''.

|-
|| Navigate to '''testutils''' directory and then to '''simulationdatabase'''.
|| Now, navigate to '''testutils''' directory and then to '''simulationdatabase'''.

|-
|| Scroll down and cursor on the '''lysozyme.pdf''' file.
|| Scroll down and notice the '''lysozyme.pdb''' file.

|-
|| Open '''lysozyme.pdb''' in a text editor.
|| Let’s open this file in a text editor.

This file is in '''PDB '''file format, and the structure of truncated '''lysozyme'''.

|-
|| Cursor on the file.
|| The file gives the coordinates in '''xyz''' axes of each atom in a molecule.

It is in the '''PDB''' format defined by '''IUPAC''' convention.

|-
|| '''Slide Number 6'''

'''Protein Data Bank'''

[https://www.rcsb.org/ https://www.rcsb.org/] '''
|| * '''Protein data bank''' is a repository of 3D structural data of biomolecules
* The website link is shown here.
* The structures are determined by '''X-ray''' diffraction, '''NMR''', & '''electron microscopy'''

|-
|| '''Slide Number 7'''

'''Protein Data Bank'''
|| Atomic resolution structures for
* Proteins, DNA and RNA
* Carbohydrates and lipids
* Several ligand molecules
are available here

|-
|| Cursor on the first 3 lines.
|| The first few lines on the top are comments, giving details about the file.

|-
|| Cursor on '''MODEL'''.
|| The '''MODEL''' indicates the first set of coordinates which is listed below it.

This happens when more than a single coordinate set is selected to represent the molecule.

|-
|| Cursor on page.
|| Learner can refer to structures determined by '''NMR''' method, to know more.

In '''NMR''' an ensemble of structure is selected to represent the molecule.

|-
|| Cursor on the '''ATOM''' lines.
|| Notice the several columns below '''MODEL'''.

Each row gives details of each '''atom''' in the biomolecule.

|-
|| Cursor on the first and second column.
|| The first column shows, it is for the atom.

The second column incrementally counts each atom in the molecule.

|-
|| Cursor on the third and fourth column.
|| Third column gives the atom name.

The next column shows the amino acid residue.

|-
|| Cursor on 5th and 6th column.
|| Fifth column is the subunit number.

Sixth column is the residue position number of the atom in the biomolecule.

|-
|| Cursor on 7, 8, and 9 columns.
|| The next three columns are the '''x, y''', and '''z''' coordinates.

They are the position of the atom in the biomolecule in 3 dimensional space.

|-
|| Cursor on the 10th column.
|| The 10th column is the occupancy of the atom at that position.

|-
|| Cursor on 11th and 12th column.
|| Then notice the '''R''' factor.

The last column lists the element that occupies the position.

|-
|| Scroll down and show '''TER''' line in the file.
|| Scroll to the end of the file and notice the '''TER''' written here.

This denotes the end of the molecular model and the molecule.

|-
|| Cursor on residue number 10.
|| Notice that, the data is truncated at the 10th residue in this document.

This file is for demonstration purpose only.

|-
|| Cursor on the interface and close the text editor.
|| All residues for '''1AKI''' which is the '''lysozyme''' entry are not present here.

Lysozyme, or full length deposition of '''1AKI''' has 129 amino acid residues.

Let’s consult the '''PDB''' site to know more.

Let’s close the text editor.

|-
|| Open web browser and go to [https://www.rcsb.org/ https://www.rcsb.org/] .
|| Next, open a web browser.

Go to the '''PDB''' website as seen here.

Let’s learn to search and download coordinates from the '''PDB''' website.

|-
|| Enter '''lysozyme''' in the search form on top and press '''Enter'''.
|| In the search form on the top, let’s enter '''lysozyme'''.

|-
|| Scroll down.
|| Scroll down the page and notice the several search results for '''lysozyme'''.

Each molecular structure that is deposited in the '''PDB''' has a unique ID.

|-
|| Scroll up and enter '''1AKI''' in the search form.
|| Now, go to the top of the page.

Click on '''Search, Basic Search'''.

Let’s search for the structure deposition ID '''1AKI'''.

|-
|| Show details of '''1AKI'''.
|| Now the structure deposition details of this protein ID, appears.
The page opens in the '''Structure Summary''' tab.

|-
|| Cursor on the page and scroll down.
|| Scroll down and notice the detailed information on this structure.

It is that of egg white '''lysozyme'''.

|-
|| Cursor on '''X-ray diffraction'''.
|| Notice that it is determined by '''X-ray diffraction''' method.

|-
|| Click on '''3D View''' tab.
Scroll to the top of the page.
|| Scroll to the top of the page and click on the '''3D View''' tab.

Scroll down the page.

An interactive window is seen on the left with the protein structure.

|-
|| Click, hold and move mouse, show protein in rotated view.
|| Click, hold and move the mouse to rotate the protein in the window.

|-
|| Cursor on primary sequence and click on 2-3 residues.

Move cursor to the protein to show the highlighted position.
|| On the top of the screen, notice the protein primary sequence.

Click on any of the residue and notice it highlighted in the structure.

|-
|| Cursor on the protein structure.
|| Currently, the secondary structure of the protein is also visible.

|-
|| Cursor on red dot.
|| All the red dots are water molecules.

Users may pause this video and explore all the details given on this '''PDB''' ID.

|-
|| Scroll up the page.
|| Let’s scroll up the page and download the molecule structure coordinate file.

|-
|| Cursor on '''Display files''' and '''Download files'''.
|| Notice the '''Display files''' and '''Download files''' pulldown towards the top right.

|-
|| Click on the '''Display files'''.
|| Click on the '''Display files''' and notice the '''FASTA''' '''Sequence''' option.

|-
|| Click on '''FASTA'''.
|| Click on it.

|-
|| Cursor on the '''FASTA''' sequence tab.
|| A new tab opens with the '''primary''' sequence of the protein in single letter code.

The first line is the header giving the ID and details about the sequence.

|-
|| Close the '''FASTA''' tab.
|| I will close this tab.

|-
|| Click on the '''PDB format''' option.
|| Next click on the '''PDB format''' option in the '''Display files''' pulldown.

|-
|| Cursor on the new tab with the '''PDB''' file.
|| Again, a new tab opens with the '''PDB''' file.

|-
|| Cursor on the header lines.
|| The first several lines are headers which give details about the deposition.

|-
|| Cursor on details on top.
|| Notice the organism, name, authors, publication details and resolution.

|-
|| Scroll down the page.
|| Scroll down the page and notice more details.

Learner may pause this video and explore the PDB file in detail.

|-
|| Cursor on '''SSBOND'''.
|| Any disulfide bond present in the protein is also listed here.

|-
||
|| Often small molecule ligand or more chains are present in the system of study.

If so, their details will also be visible in the header.

|-
|| Cursor on the atomic coordinates.
|| The coordinates for each atom in the unit structure is listed below.

|-
|| Cursor on the atomic coordinates.
|| Notice that there are no hydrogens listed here.

This is because the x-ray diffraction method does not detect hydrogens.

|-
|| Screenshot of '''1AKI''' file opened in text editor.
|| The '''1AKI''' file, which we opened earlier, had hydrogen atoms added to the file.

That file also has a trimmed header.

Hydrogen atoms are added to the molecule afterwards as needed by the users.

|-
|| Scroll down.

Cursor at '''TER'''.
|| Now, scroll almost to the end of the page.

|-
|| Cursor on '''HETATM'''.

Point to the HOH atoms in the file.
|| Below '''TER''' tag, this there are many hetero atoms listed now.

They are water molecules that are present in the protein crystal.

|-
|| Show '''O''' element for '''HETATM'''.
|| Notice that, here too, hydrogens will not be observed.

|-
|| Show '''O''' element for '''HETATM'''.
|| Often, these water molecules are removed from the PDB file, before simulation.

|-
|| Close the '''PDB''' details tab.
|| Let’s close the '''PDB''' details tab.

|-
|| Click on the '''Download Files''' pulldown.
|| Now, click on the '''Download Files''' pulldown.

|-
|| Choose the '''PDB format'''.
|| Choose the '''PDB format'''.

A dialog box may or may not open prompting to save the file.

|-
|| Choose '''Save File''' and click on '''Ok'''.
|| If so, choose to save the file on the computer and click on '''Ok'''.

Allow the file download to complete.

|-
|| Cursor on the PDB web page.
|| Learner may pause this video and open the downloaded file in a text editor.

Notice that the file we viewed and downloaded are the same.

|-
|| Cursor on the PDB web page.
|| Open the '''PDB''' file in '''VMD''' or another molecular viewer.

Notice the structure displayed.

|-
|| '''Slide Number 8'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* The '''PDB''' file format
* The '''PDB''' website
* '''FASTA''' file format
* Header details in '''PDB''' file
* Downloaded a '''pdb''' file

|-
|| '''Slide Number 9'''

'''Assignment '''
|| For assignment activity, please do the following.

* Go through the '''PDB''' website
* Familiarize with more details given for the PDB deposition.
* Go through the header details of the file that is downloaded.

|-
|| '''Slide Number 10'''

'''Assignment '''
|| Go through the given IDs from '''PDB''' website for enzyme '''DHFR''' and it’s complexes.

* '''2L28''' for '''apo enzyme''' and multiple '''conformer'''s
* '''1DIS''' for '''binary''' complex
* '''3DAT''' for '''ternary''' complex

|-
|| '''Slide Number 11'''

'''Assignment '''
||
* Notice the presence and absence of hydrogen atoms in the structure files
* Familiarize with
** Conformational changes in the enzyme
** Hydrogen bonding with ligands

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
|| '''Slide Number 14'''

'''Forum for questions'''

|| Post your timed queries in this forum.

|-
|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

|-
||
|| This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

Gromacs/C2/PDB-File-Format-and-Website/English

2021-10-21T13:07:57Z

Ranipv076:

{| border =1
|| '''Visual Cue'''
|| '''Narration'''

|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial on '''PDB File Format and Website'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn,

* About PDB file format for molecular structure
* Protein Data Bank ('''PDB''') website
* Download a '''pdb''' file from '''PDB''' website
* About '''FASTA''' file format

|-
|| '''Slide Number 3'''

'''System and Software Requirement'''
|| To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' v3.36.2
* A working internet connection to access the '''PDB''' website

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* For pre-requisite tutorials, please visit this site.

|-
|| '''Slide Number 5'''

'''File from downloaded tarball'''
|| Files used in this tutorial, can be found in the,
* Downloaded and extracted tarball directory used for '''Gromacs''' installation

|-
|| Open the File manager.
|| Let’s open the '''File manager'''.

Go to the downloaded and extracted tarball directory for '''Gromacs''' installation.

|-
|| Cursor on the files of the extracted '''Gromacs''' directory.

Go to '''src''' directory.
|| Few test '''PDB''' files are given for testing purposes with '''Gromacs''' installation.

They can be found in the '''src''' directory of the extracted tarball of '''Gromacs'''.

|-
|| Navigate to '''testutils''' directory and then to '''simulationdatabase'''.
|| Now, navigate to '''testutils''' directory and then to '''simulationdatabase'''.

|-
|| Scroll down and cursor on the '''lysozyme.pdf''' file.
|| Scroll down and notice the '''lysozyme.pdb''' file.

|-
|| Open '''lysozyme.pdb''' in a text editor.
|| Let’s open this file in a text editor.

This file is in '''PDB '''file format, and the structure of truncated '''lysozyme'''.

|-
|| Cursor on the file.
|| The file gives the coordinates in '''xyz''' axes of each atom in a molecule.

It is in the '''PDB''' format defined by '''IUPAC''' convention.

|-
|| '''Slide Number 6'''

'''Protein Data Bank'''

[https://www.rcsb.org/ https://www.rcsb.org/] '''
|| * '''Protein data bank''' is a repository of 3D structural data of biomolecules
* The website link is shown here.
* The structures are determined by '''X-ray''' diffraction, '''NMR''', & '''electron microscopy'''

|-
|| '''Slide Number 7'''

'''Protein Data Bank'''
|| Atomic resolution structures for
* Proteins, DNA and RNA
* Carbohydrates and lipids
* Several ligand molecules
are available here

|-
|| Cursor on the first 3 lines.
|| The first few lines on the top are comments, giving details about the file.

|-
|| Cursor on '''MODEL'''.
|| The '''MODEL''' indicates the first set of coordinates which is listed below it.

This happens when more than a single coordinate set is selected to represent the molecule.

|-
|| Cursor on page.
|| Learner can refer to structures determined by '''NMR''' method, to know more.

In '''NMR''' an ensemble of structure is selected to represent the molecule.

|-
|| Cursor on the '''ATOM''' lines.
|| Notice the several columns below '''MODEL'''.

Each row gives details of each '''atom''' in the biomolecule.

|-
|| Cursor on the first and second column.
|| The first column shows, it is for the atom.

The second column incrementally counts each atom in the molecule.

|-
|| Cursor on the third and fourth column.
|| Third column gives the atom name.

The next column shows the amino acid residue.

|-
|| Cursor on 5th and 6th column.
|| Fifth column is the subunit number.

Sixth column is the residue position number of the atom in the biomolecule.

|-
|| Cursor on 7, 8, and 9 columns.
|| The next three columns are the '''x, y''', and '''z''' coordinates.

They are the position of the atom in the biomolecule in 3 dimensional space.

|-
|| Cursor on the 10th column.
|| The 10th column is the occupancy of the atom at that position.

|-
|| Cursor on 11th and 12th column.
|| Then notice the '''R''' factor.

The last column lists the element that occupies the position.

|-
|| Scroll down and show '''TER''' line in the file.
|| Scroll to the end of the file and notice the '''TER''' written here.

This denotes the end of the molecular model and the molecule.

|-
|| Cursor on residue number 10.
|| Notice that the data is truncated at the 10th residue in this document.

This file is for demonstration purpose only.

|-
|| Cursor on the interface and close the text editor.
|| All the residues for '''1AKI''' are not present here.

Lysozyme, or full length deposition of '''1AKI''' has 129 amino acid residues.

Let’s consult the '''PDB''' site to know more.

Let’s close the text editor file.

|-
|| Open web browser and go to [https://www.rcsb.org/ https://www.rcsb.org/] .
|| Next, open a web browser.

Go to the '''PDB''' website as seen here.

Let’s learn to search and download coordinates from the '''PDB''' website.

|-
|| Enter '''lysozyme''' in the search form on top and press '''Enter'''.
|| In the search form on the top, let’s enter '''lysozyme'''.

|-
|| Scroll down.
|| Scroll down the page and notice the several search results for '''lysozyme'''.

Each molecular structure that is deposited in the '''PDB''' has a unique ID.

|-
|| Scroll up and enter '''1AKI''' in the search form.
|| Now, go to the top of the page.

Click on '''Search, Basic Search'''.

Let’s search for the structure deposition ID '''1AKI'''.

|-
|| Show details of '''1AKI'''.
|| Now the structure deposition details of this protein ID, appears.
The page opens in the '''structure summary''' tab.

|-
|| Cursor on the page and scroll down.
|| Scroll down and notice the detailed information on this structure.

It is that of egg white '''lysozyme'''.

|-
|| Cursor on '''X-ray diffraction'''.
|| Notice that it is determined by '''X-ray diffraction''' method.

|-
|| Click on '''3D View''' tab.
Scroll down the page.
|| Scroll to the top of the page and click on the '''3D View''' tab.

Scroll down the page.

An interactive window on the left with the protein structure.

|-
|| Click, hold and move mouse, show protein in rotated view.
|| Click, hold and move the mouse to rotate the protein in the window.

|-
|| Cursor on primary sequence and click on 2-3 residues.

Move cursor to the protein to show the highlighted position.
|| On the top of the screen, notice the protein primary sequence.

Click on any of the residue and notice it highlighted in the structure.

|-
|| Cursor on the protein structure.
|| Currently, the secondary structure of the protein is also visible.

|-
|| Cursor on red dot.
|| All the red dots are water molecules.

Users may pause this video and explore all the details given on this '''PDB''' ID.

|-
|| Scroll up the page.
|| Let’s scroll up the page and download the molecule structure coordinate file.

|-
|| Cursor on '''Display files''' and '''Download files'''.
|| Notice the '''Display files''' and '''Download files''' pulldown towards the top right.

|-
|| Click on the '''Display files'''.
|| Click on the '''Display files''' and notice the '''FASTA''' '''Sequence''' option.

|-
|| Click on '''FASTA'''.
|| Click on it.

|-
|| Cursor on the '''FASTA''' sequence tab.
|| A new tab opens with the '''primary''' sequence of the protein in single letter code.

The first line is the header giving the ID and details about the sequence.

|-
|| Close the '''FASTA''' tab.
|| I will close this tab.

|-
|| Click on the '''PDB format''' option.
|| Next click on the '''PDB format''' option in the '''Display files''' pulldown.

|-
|| Cursor on the new tab with the '''PDB''' file.
|| Again, a new tab opens with the '''PDB''' file.

|-
|| Cursor on the header lines.
|| The first several lines are headers which give details about the deposition.

|-
|| Cursor on details on top.
|| Notice the organism, name, authors, publication details and resolution.

|-
|| Scroll down the page.
|| Scroll down the page and notice more details.

Learner may pause this video and explore the PDB file in detail.

|-
|| Cursor on '''SSBOND'''.
|| Any disulfide bond present in the protein is also listed here.

|-
||
|| Often small molecule ligand or more chains are present in the system of study.

If so, their details will also be visible in the header.

|-
|| Cursor on the atomic coordinates.
|| The coordinates for each atom in the unit structure is listed below.

|-
|| Cursor on the atomic coordinates.
|| Notice that there are no hydrogens listed here.

This is because the x-ray diffraction method does not detect hydrogens.

|-
|| Screenshot of '''1AKI''' file opened in text editor.
|| The '''1AKI''' file, which we opened earlier, had hydrogen atoms added to the file.

That file also has a trimmed header.

Hydrogen atoms are added to the molecule afterwards as needed by the users.

|-
|| Scroll down.

Cursor at '''TER'''.
|| Now, scroll almost to the end of the page.

|-
|| Cursor on '''HETATM'''.

Point to the HOH atoms in the file.
|| Below '''TER''' tag, this there are many hetero atoms listed now.

They are water molecules that are present in the protein crystal.

|-
|| Show '''O''' element for '''HETATM'''.
|| Notice that, here too, hydrogens will not be observed.

|-
|| Show '''O''' element for '''HETATM'''.
|| Often, these water molecules are removed from the PDB file, before simulation.

|-
|| Close the '''PDB''' details tab.
|| Let’s close the '''PDB''' details tab.

|-
|| Click on the '''Download Files''' pulldown.
|| Now, click on the '''Download Files''' pulldown.

|-
|| Choose the '''PDB format'''.
|| Choose the '''PDB format'''.

A dialog box may or may not open prompting to save the file.

|-
|| Choose '''Save File''' and click on '''Ok'''.
|| If so, choose to save the file on the computer and click on '''Ok'''.

Allow the file download to complete.

|-
|| Cursor on the PDB web page.
|| Learner may pause this video and open the downloaded file in a text editor.

Notice that the file we viewed and downloaded are the same.

|-
|| Cursor on the PDB web page.
|| Open the '''PDB''' file in '''VMD''' or another molecular viewer.

Notice the structure displayed.

|-
|| '''Slide Number 8'''

'''Summary '''
|| Now let’s summarize. In this tutorial, we learned about,

* The '''PDB''' file format
* The '''PDB''' website
* '''FASTA''' file format
* Header details in '''PDB''' file
* Downloaded a '''pdb''' file

|-
|| '''Slide Number 9'''

'''Assignment '''
|| For assignment activity, please do the following.

* Go through the '''PDB''' website
* Familiarize with more details given for the PDB deposition.
* Go through the header details of the file that is downloaded.

|-
|| '''Slide Number 10'''

'''Assignment '''
|| Go through the given IDs from '''PDB''' website for enzyme '''DHFR''' and it’s complexes.

* '''2L28''' for '''apo enzyme''' and multiple '''conformer'''s
* '''1DIS''' for '''binary''' complex
* '''3DAT''' for '''ternary''' complex

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|| '''Slide Number 11'''

'''Assignment '''
||
* Notice the presence and absence of hydrogen atoms in the structure files
* Familiarize with
** Conformational changes in the enzyme
** Hydrogen bonding with ligands

|-
|| '''Slide Number 12'''

'''Spoken Tutorial Project'''
|| This video summarises the Spoken Tutorial Project.

Please download and watch it.

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|| '''Slide Number 13'''

'''Spoken Tutorial workshops'''
|| We conduct workshops using spoken tutorials and give certificates.

Please write to us.

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|| '''Slide Number 14'''

'''Forum for questions'''

|| Post your timed queries in this forum.

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|| '''Slide Number 15'''

'''Acknowledgment'''
|| Spoken Tutorial Project is funded by MoE, Government of India.

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||
|| This is Rani from IIT, Bombay. Thank you for joining.

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|}