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