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Information

Purpose: Molecular Dynamics
Latest version: 2018.3
License: GNU LGPL
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

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 external 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 --nodes=1
#SBATCH --ntasks=24
#SBATCH --mem=4G

module load apps/gromacs/2018.1

INPUT_DIR=${SLURM_SUBMIT_DIR}
OUTPUT_DIR=${SLURM_SUBMIT_DIR}

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 (.tpr .tpb .tpa).
    • Contains the topology of the system.
  • -g: Output log file.
  • -o: Output trajectory file (.trr .cpt .trj .tng).
    • 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 simulation of a protein with Gromacs to get hands-on with the program.



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