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GROMACS on Qarnot – documentation


by Tiphaine Bonniot - October 7, 2021 - Biotech

Introduction

GROMACS is one of the fastest and most popular molecular dynamics software packages. It is mainly designed for molecular dynamics simulations of proteins, lipids, and nucleic acids. It is free and open-source and can run on central processing units (CPUs) and graphics processing units (GPUs).

Versions

The test case uses a GROMACS version in the 2021 series.

Release year Version
2021 2021.2 2021.2

If you are interested in another version, please send us an email at qlab@qarnot.com.

Prerequisites

Before launching the case, please ensure that the following prerequisites have been met.

Test case

This test case is based on Justin A. Lemkul, Ph.D.’s lysozyme in water tutorial simulation. You can find the tutorial here. The the mdp files, the pdb file from the Protein Data Bank and the the script to launch the simulation can be downloaded all at once from here. Unzip the lysozyme-in-water.zip folder to be able to use it on Qarnot.

Lysozyme 1aki protein – RCSB Protein Data Bank, rendered by VMD

Copy the following code in a sh script and place it in the lysozyme-in-water folder you unzipped before. It contains GROMACS instructions to run the simulation.

run_md.sh

The reader can visit Lysozyme in water GROMACS Tutorial for more information about this script and results interpretation.

Launching the case

Copy the following code in a Python script and save it next to the lysozyme-in-water folder. Be sure you have copied your authentication token in the script (instead of <<<MY_SECRET_TOKEN>>>) to be able to launch the task on Qarnot.

gromacs.py

Make sure that all input files mentioned above (1 pdb file, 5 mdp files, 1 sh file) are in the same folder named lysozyme-in-water. Your working directory should look like this :

  • lysozyme-in-water/
    • 1aki.pdb : protein structure file (egg white lyzozyme) from the RCSB protein data bank
    • ions.mdp : parameters to generate atomic description of the system
    • minim.mdp : parameters to relax the system (energy minimization)
    • nvt.mdp : parameters to stabilize the temperature of the system (nvt simulation)
    • npt.mdp : parameters to stabilize the pressure of the system (npt simulation)
    • md.mdp : parameters to run the molecular dynamics simulation
    • run_md.sh : script to run the molecular dynamics simulation using GROMACS
  • gromacs.py : python script to run the simulation on Qarnot

To launch this script, open a terminal in your working directory and execute python3 gromacs.py &. It will launch the execution of run_md.sh on Qarnot and wait in the background until the execution is over to download the results (it can take up to 1h).

Results

At any given time, you can monitor the status of your task on the Console. You should now have an output folder in your working directory on your computer and a gromacs-out bucket on Qarnot’s Console containing all output files. You can for instance open the md_0_1.gro file to view the final result in using a viewing program such as VMD or with an online gro files visualizer such as Groview.

Lysozyme 1aki protein in water, rendered by VMD

The GROMACS molecular dynamics simulation has several output files in the output folder. For more information, see the Analysis part of the Lysozyme in Water – GROMACS Tutorial by Justin A. Lemkul, Ph.D.

Wrapping up

That’s it! If you have any questions, please contact qlab@qarnot.com and we will help you with pleasure! You can read more about bio-technology use cases on Qarnot here : Molecular docking and cloud computing – Qarnot Blog or here : Nucleotide sequence alignment with blastn – Qarnot Blog.

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