Software: 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.
Available Versions
Bell: | 2020.3 2022.3.amd1 |
---|---|
Negishi: | 2020.3 2022.3.amd1 |
Module
You can load the modules by:
module load rocmcontainers
module load 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