GROMACS
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GROMACS v2.12
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.