GROMACS

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.

More information: http://www.gromacs.org

Running GROMACS

Module Version
GROMACS 2016.3-foss-2017a
2016.3-intel-2017a
2016.5-intel-2018a

To see available versions when logged into Fram issue command

module spider gromacs

To use GROMACS type

module load GROMACS/<version>

specifying one of the available versions in the table above.

Sample GROMACS Job Script

#!/bin/bash
#SBATCH --account=nnNNNNk
#SBATCH --job-name=topol
#SBATCH --time=1-0:0:0
#SBATCH --nodes=10

## Recommended safety settings:
set -o errexit # Make bash exit on any error
set -o nounset # Treat unset variables as errors

module restore system
module load GROMACS/<version>

case=$SLURM_JOB_NAME

## Prepare input files
cp $case.tpr $SCRATCH
cd $SCRATCH

mpirun gmx_mpi mdrun $case.tpr

## Copy results back to the submit directory
cleanup "cp $SCRATCH/* $SLURM_SUBMIT_DIR"

License Information

GROMACS is available under the GNU Lesser General Public License (LGPL), version 2.1.

It is the user's responsibility to make sure they adhere to the license agreements.

Citation

When publishing results obtained with the software referred to, please do check the developers web page in order to find the correct citation(s).

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