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Gromacs

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.

Gromacs website

Installed version​

$ module avail gromacs

gromacs-2023.1/double/openmpi-4.1.5/gcc-13.1.0-openblas

Build options:

  • Custom blas/lapack using OpenBlas
  • double precision enabled
  • MPI with OpenMPI

Slurm script​

Please modify this script as required:

gromacs.slurm
#!/bin/bash -l

## Job Script script to be adapted as required ##

#SBATCH --job-name="MY_JOB_NAME" ## <---(modify me)
#SBATCH --output=%x.%J.out       ## %x=job name, %J=job id
#SBATCH --error=%x.%J.out
#SBATCH --time 24:00:00          ## 24h walltime ((hh:mm::ss)  <--- (modify me)
#SBATCH --partition=mpi1         ## mpi1 partition <---(modify me)
#SBATCH --ntasks=48              ## request 48 MPI tasks <---(modify me)
#SBATCH --mem=0                  ## request all node memory
#SBATCH --mail-user=<yourmail>@.yourdomain.fr   ##  <---(modify me)
#SBATCH --mail-type=END,FAIL     ## notify when job end/fail

## We strongly recommend using this command
module purge

module load gromacs-2023.1/double/openmpi-4.1.5/gcc-13.1.0-openblas

srun gmx_mpi_d mdrun_mpi -s test.tpr

Submit job to Slurm:

$ sbatch gromacs.slurm