gromacs¶

Description¶

GROMACS GROningen MAchine for Chemical Simulations is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.

Versions¶

Scholar: 2018.2, 2020.2, 2021, 2021.3
Gilbreth: 2018.2, 2020.2, 2021, 2021.3
Anvil: 2018.2, 2020.2, 2021, 2021.3

Module¶

You can load the modules by:

module load ngc
module load gromacs

Example job¶

Warning

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 myallocation     # Allocation name
#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 ngc gromacs