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. More info on GROMACS can be found at http://www.gromacs.org/ For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:gromacs
Versions
2018.2
2020.2
2021.3
2021
Commands
gmx
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 --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