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A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Description

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles

Read more on the GROMACS home page.

For a manual consult the the GROMACS home page.

Modules

VersionInstallation Pathmodulefilecompilercomment
2018.4/sw/chem/gromacs/2018.4/skl/impigromacs/2018.4intelmpi
2018.4/sw/chem/gromacs/2018.4/skl/impi-plumedgromacs/2018.4-plumedintelmpiwith plumed
2019.6/sw/chem/gromacs/2019.6/skl/impigromacs/2019.6intelmpi
2019.6/sw/chem/gromacs/2019.6/skl/impi-plumedgromacs/2019.6-plumedintelmpiwith plumed

Usage

Load the necessary modulefiles. Note that Intel MPI module file should be loaded first

module load impi/2018.5 gromacs/2018.4

This provides access to the binary gmx_mpi wich can be used to run simulations with sub-commands as gmx_mpi mdrun

In order to run simulations MPI runner should be used: 

mpirun gmx_mpi mdrun MDRUNARGUMENTS

Job Script Examples

For Intel Cascade Lake compute nodes – simple case of a GROMACS job using a total of 960 CPU cores distributed over 10 nodes running 96 tasks each for 12 hours

#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH -p standard96
#SBATCH -N 10
#SBATCH --tasks-per-node 96

export SLURM_CPU_BIND=none

module load impi/2019.5
module load gromacs/2019.6

mpirun gmx_mpi mdrun MDRUNARGUMENTS


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