gromacs

Link to section 'Description' of 'gromacs' Description

GROMACS is a molecular dynamics application designed to simulate Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed to simulate biochemical molecules like proteins, lipids, and nucleic acids that have a lot of complicated bonded interactions.

Link to section 'Versions' of 'gromacs' Versions

Bell: 2020.3, 2022.3.amd1
Negishi: 2020.3, 2022.3.amd1

Link to section 'Module' of 'gromacs' Module

You can load the modules by:

module load rocmcontainers
module load gromacs

Link to section 'Example job' of 'gromacs' Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run gromacs on our clusters:

#!/bin/bash
#SBATCH -A gpu
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --gpus-per-node=1
#SBATCH --job-name=gromacs
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml rocmcontainers gromacs