Difference between revisions of "Gromacs/C3/Temperature-and-Pressure-Equilibration/English"

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(Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the tutorial '''Temperature and Pressure Equilibration'''. |-...")
 
 
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[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
 
[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
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|| To follow this tutorial, * Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
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|| To follow this tutorial,  
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* Learner must be familiar with basics of '''Gromacs''' and '''VMD'''.
 
* For pre-requisite tutorials, please visit this site.
 
* For pre-requisite tutorials, please visit this site.
  
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Notice the two mdp files provided.
 
Notice the two mdp files provided.
  
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Copy the mdp files to the working directory.
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Copy the mdp file to the working directory.
  
 
|-
 
|-
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Cursor on 50000 steps.
 
Cursor on 50000 steps.
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|| This is a short simulation for 100 ps with each step having 2 fs.  
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|| This is a short simulation for 100 ps with each step having 2 femtoseconds.  
  
 
Hence there are 50000 steps.
 
Hence there are 50000 steps.
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|-
 
|-
 
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
 
|| Cursor on '''temperature''' and '''pcoupl '''parameters.
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|| Here, temperature is set to 300K.
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|| Here, temperature is set to 300 '''Kelvin'''.
  
  
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|-
 
|-
 
|| 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] '''
 
|| 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] '''
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|| Details on choosing them can be accessed from the '''Gromacs''' documentation.  
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|| Details on choosing the parameters can be accessed from the '''Gromacs''' documentation.  
  
 
|-
 
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|-
 
|-
 
|| Cursor on the -r flag.
 
|| Cursor on the -r flag.
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|| The r flag is used only when position restraint is used in the '''mdp''' file.
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|| If the r flag is used, then position must be restrained.
  
−
Go through the additional materials section to know more.
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Pause the video and go through the additional materials section to know more.
 +
 
 +
Go through the '''Gromacs''' manual for detailed understanding.
  
 
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|-
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'''Computation Time'''
 
'''Computation Time'''
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|| * Having more steps in MD takes longer time.
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||  
 +
* Having more steps in MD takes longer time.
 
* Use a computing facility to run these processes.
 
* Use a computing facility to run these processes.
 
* Take care not to overheat or burn your computer.
 
* Take care not to overheat or burn your computer.
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Show files copied in the working directory.
 
Show files copied in the working directory.
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|| An additional file '''gro''' will be created at the completion of the process.
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|| An additional '''gro''' file will be created at the completion of the process.
  
 
Copy the '''nvt''' files provided for analysis to continue further.
 
Copy the '''nvt''' files provided for analysis to continue further.
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|-
 
|-
 
|| Cursor on the graph.
 
|| Cursor on the graph.
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|| Notice that, the temperature fluctuates around 300 K.
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|| Notice that, the temperature fluctuates around 300 '''Kelvin'''.
  
 
Velocity variation in the system is given by '''Maxwell-Boltzmann'''  
 
Velocity variation in the system is given by '''Maxwell-Boltzmann'''  
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|-
 
|-
 
|| Cursor on '''npt.gro'''.
 
|| Cursor on '''npt.gro'''.
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|| '''npt.gro''' is the output system from all the prior processes.
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|| '''npt.gro''' is the output system configuration from all the prior processes.
  
 
|-
 
|-
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|-
 
|-
 
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
 
|| Type, '''xmgrace pressure.xvg''' and press '''Enter'''.
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|| I will plot the '''dot''' '''xvg''' using '''Grace''' as seen.
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|| I will plot the '''pressure dot''' '''xvg''' using '''Grace''' as seen.
  
 
Notice the fluctuations.  
 
Notice the fluctuations.  
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* Ensemble properties and equilibration
 
* Ensemble properties and equilibration
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* Run '''NVT''' and temperature equilibration
+
* Performed '''NVT''' and temperature equilibration
−
* Plotted the temperature fluctuation to check for equilibration
+
* Plotted the temperature fluctuation and checked for equilibration
 
* '''NPT''' and pressure equilibration
 
* '''NPT''' and pressure equilibration
 
* Plotted the pressure fluctuation
 
* Plotted the pressure fluctuation
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* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
 
* Plot density and volume of the system after '''NVT''' and '''NPT''' steps.
−
* Recap processes and commands from '''1AKI.pdb''' to equilibration.
+
* Recap processes and commands starting from '''1AKI.pdb''' to equilibration.
 
* Read publications of your choice using '''Gromacs'''.
 
* Read publications of your choice using '''Gromacs'''.
−
 
  
 
|-
 
|-

Latest revision as of 19:39, 21 February 2022

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

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 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.

Contributors and Content Editors

Ranipv076

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