Difference between revisions of "Gromacs/C3/Temperature-and-Pressure-Equilibration/English"
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* Ensemble properties and equilibration | * Ensemble properties and equilibration | ||
| − | * | + | * Performed '''NVT''' and temperature equilibration |
| − | * Plotted the temperature fluctuation | + | * Plotted the temperature fluctuation and checked for equilibration |
* '''NPT''' and pressure equilibration | * '''NPT''' and pressure equilibration | ||
* Plotted the pressure fluctuation | * Plotted the pressure fluctuation | ||
| Line 426: | Line 426: | ||
* Recap processes and commands from '''1AKI.pdb''' to equilibration. | * Recap processes and commands from '''1AKI.pdb''' to equilibration. | ||
* Read publications of your choice using '''Gromacs'''. | * Read publications of your choice using '''Gromacs'''. | ||
| − | |||
|- | |- | ||
Revision as of 14:32, 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,
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| Slide Number 3
System and Software Requirement |
To record this tutorial, I am using
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| Slide Number 4
Pre-requisites |
To follow this tutorial,
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| Slide Number 5
Code Files |
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| 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 |
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| Slide Number 7
Pressure and Temperature |
* Here, ensemble consists of all the particles in the system
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| Show files in file manager for firstmd directory.
|
Let’s open the provided nvt.mdp file in a text editor. |
| Show nvt.mdp in the text editor.
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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.
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| 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 |
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| 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,
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| Slide Number 10
Assignment |
For assignment activity, please do the following.
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| Slide Number 11
Assignment |
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| Slide Number 12
Spoken Tutorial Project |
This video summarises the Spoken Tutorial Project.
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| Slide Number 13
Spoken Tutorial workshops |
We conduct workshops using spoken tutorials and give certificates.
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| 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. |
