Gromacs

Introduction

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. This container, based on a released version of GROMACS, is an AMD beta version with ongoing optimizations. This container only supports up to a 4 GPU configuration. For more information, please check: Home page: https://www.gromacs.org Docker: https://www.amd.com/en/technologies/infinity-hub/gromacs

Versions

  • 2020.3

Commands

  • gmx

  • gmx_mpi

  • demux.pl

  • xplor2gmx.pl

  • mpirun

  • mpiexec

  • ompi_info

Module

You can load the modules by:

module load rocmcontainers
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 --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