Snehalathak at 06:58, 21 January 2022

2022-01-21T06:58:01Z

Snehalathak at 06:56, 21 January 2022

2022-01-21T06:56:12Z

Ranipv076: Created page with " {| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Energy Minimization'''. |- | | '''S..."

2021-12-14T07:21:34Z

Created page with " {| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Energy Minimization'''. |- | | '''S..."

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{| 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.

|-
|}

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 Copy the files provided for analysis to continue further.
-An additional gro files will be created at the completion of the process.
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 |-

Gromacs/C3/Energy-Minimization/English - Revision history

Snehalathak at 06:58, 21 January 2022

Snehalathak at 06:56, 21 January 2022

Ranipv076: Created page with " {| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Energy Minimization'''. |- | | '''S..."