View source for Gromacs/C3/Temperature-and-Pressure-Equilibration/English


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|| '''Visual Cue'''
|| '''Narration'''
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|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the tutorial '''Temperature and Pressure Equilibration'''.

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|| '''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''' 

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|| '''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.

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|| '''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

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|| '''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.

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|| 
|| As done in the energy minimization step, we will enter the next commands.

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|| 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.

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|| 
|| You may also pause the tutorial and allow the process to complete.

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|| 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.

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|| Cursor on '''nvt.trr''', '''nvt.log''' and nvt.edr files.
|| '''Trajectory''', '''log''' and '''edr''' files are also created in this process.

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|| 
|| Delete the files from this aborted process.

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|| Show file deletion.
|| If you have completed the process, do not delete the files.

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|| 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.

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|| 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.

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|| 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.

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|| 
|| 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.

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|| 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.

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|| Close '''grace'''.

Go to the '''terminal'''.
|| Let’s close '''grace'''.

Go back to the '''terminal'''.

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|| 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'''.

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|| 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'''.

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|| '''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'''.


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|| '''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.

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