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Information

Purpose: Molecular Dynamics
Latest version: 2018.1
License: GNU LGPL
Website: http://www.gromacs.org/ extlink-icon

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

For more information use 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 documentation 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 --nodes=1
#SBATCH --ntasks=24
#SBATCH --mem=4G

module load apps/gromacs/2018.1

INPUT_DIR=${PWD}
OUTPUT_DIR=${PWD}

cd $SCRATCH
cp -r $INPUT_DIR $SCRATCH
 
mpirun -np $SLURM_NTASKS \
  gmx_mpi mdrun \
  -s gromacs_example.trp \
  -g gromacs_example.log \
  -o gromacs_example.cpt \
  -c gromacs_example.gro \
  -e gromacs_example.edr

cp ./* $OUTPUT_DIR

Sbatch options:

  • -J: Specify a name for the job allocation. The default is the name of the batch script.
  • -e: Specify a name for the error output file.
  • -o: Specify a name for the output file.
  • -p: Specify the name of the partition (queue) where the job will be submited. The default is std.
  • --nodes: Number of nodes requested for allocation.
  • --ntasks: Number of processes requested for allocation.
  • --mem-per-cpu: Memory allocated per core.

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. It contains the topology of the system.
  • -g: Output log file.
  • -o: Output trajectory file. It contains coordinates, velocities and optionally forces.
  • -c: Output structure file. It contains the coordinates and velocities of last step.
  • -e: Output energy file. It contains energies, temperature, pressure, etc.

 

 

Tutorial

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

 

 

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