GROMACS

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GROMACS 2016.5

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/2018.2
module load intelmpi/2018.2
module load gromacs/2016.5

# DIRECTORY TO RUN - $PBS_O_WORKDIR 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. As such running on CC systems which have GPUs, such as Graham and Cedar, is recommended.