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.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: March 14 2026 09:24:13.