GROMACS

GROMACS 2018.6

GROMACS is a versatile molecular dynamics package. A thorough treatment of GROMACS can be found on the Compute Canada page. Here is a sample Niagara run script:

#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=4
#SBATCH --time=11:00:00
#SBATCH --job-name test

module load intel/2019u3
module load intelmpi/2019u3
module load gromacs/2018.6

# DIRECTORY TO RUN - $SLURM_SUBMIT_DIR is directory job was submitted from
cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
 
srun gmx_mpi mdrun -deffnm md

The above script requests 1 node and runs gromacs in a hybrid mode, in 10 groups of 4 processors.

Note that GROMACS is well-suited to use on GPUs, of which Niagara has none. Running on Mist is recommended. Alternatively, running on CC systems which have GPUs, such as Graham and Cedar, is also an option.

Gromacs on Mist GPU cluster

See details on Mist page: Gromacs on Mist