Purpose: Molecular Dynamics
Latest version: 2021.3
License: (tick) Free of use
                 GNU LGPL _ext-link
Website: http://www.gromacs.org/ _ext-link

Gromacs is a program for general molecular dynamics, notable for its fast computation of 1-4 interactions.

It can implement regular molecular dynamics simulations using a variety of integrators, Langevin dynamics, energy minimisation, test-particle insertion, etc. It implements a variety of methods to calculate electrostatics and Van der Waals interactions, thermostats and barostats, 2- and 3-dimensional periodic boundary conditions, etc.

SLURM Submit script example

More information about the submit script can be found using the Job Script Generator.

For optimal performance, before a long production run, you are advised to experiment with different thread allocations to PME and DD tasks, using mdrun options. Please refer to the Gromacs documentationext-link for more details.

gromacs_example.slm
#!/bin/bash
#SBATCH -J gromacs_example
#SBATCH -e gromacs_example.err
#SBATCH -o gromacs_example.out
#SBATCH -p std
#SBATCH --ntasks=24

module load apps/gromacs/2019.1
 
##
#  Modify the input and output files!
cp -r ${SLURM_SUBMIT_DIR}/*.trp ${SCRATCH}
cd ${SCRATCH}
 
srun gmx_mpi mdrun \
  -s gromacs_example.tpr \
  -g gromacs_example.log \
  -o gromacs_example.trr \
  -c gromacs_example.gro \
  -e gromacs_example.edr
 
cp ./{*.log,*.cpt,*.gro,*.edr} ${SLURM_SUBMIT_DIR}

Sbatch options:

The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.

  • -J: Name for the job's allocation.
  • -e: Name of the sterr redirection filename.
  • -o: Name of the stdout redirection filename.
  • -p: Name of the partition (queue) where the job will be submited.

  • -n: Number of tasks.

  • -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.


Software execution information:

The mdrun program is the main program of Gromacs. It can perform Molecular Dynamics, Stochastic Dynamics, Energy Minimisation, test particle insertion or (re)calculation of energies.

  • -s: Input file (.tpr .tpb .tpa).
    • Contains the topology of the system.
  • -g: Output log file.
  • -o: Output trajectory file (.trr .cpt .trj .tng). Use .trr for full-precision data.
    • Contains coordinates, velocities and, optionally, forces.
  • -c: Output structure file (.gro .g96 .pdb .brk .ent .esp).
    • Contains the coordinates and velocities of last step.
  • -e: Output energy file (.edr).
    • Contains energies, temperature, pressure, etc.


Tutorial

You can follow this tutorial about a protein's simulation using Gromacs to get hands-on with the program.




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