GROMACS

See the GROMACS Tutorial Lysosome in Water, to get started.

Copy the example files from /home/gwhowell/apps/samples/gromacs/lysozyme and then cd to lysozyme.

Create a submission script called bmdrun containing the following:

The script is very similar to the bmdrun2016 file in the lysozyme folder. Only the "qc" resource has been removed.

#!/bin/bash
#SBATCH --ntasks=2
#SBATCH --ntasks-per-node=2
#SBATCH --time=00:20:00
#SBATCH --output=out.%j
#SBATCH --error=err.%j
source /usr/local/apps/gromacs/gromacs2016-int2016.csh
srun gmx_mpi mdrun -v -deffnm em

To submit the job, type

sbatch bmdrun

Last modified: May 03 2026 12:56:12.