GROMACS
Introduction
GROMACS is a versatile package for molecular dynamics simulations, which solves the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS has been primarily designed for biochemical molecules (such as proteins, lipids and nucleic acids) but has also been used for research on non-biological systems, e.g. polymers. This is a CPU only build, containing both MPI and threadMPI builds.
CPU Version:
GROMACS/2020.4-foss-2020a
GPU versions:
GROMACS/2020-fosscuda-2019b
GROMACS/2020.4-foss-2020a-PLUMED-2.6.2
The guide shows how to
prepare a GROMACS job submission script and
submit the GROMACS job.
GROMACS on ARC clusters
Several versions of GROMACS are installed on the ARC clusters, mostly with only single precision support. GROMACS is managed through the module
utility; use module spider gromacs
to see the modules available, and also use module
to load the appropriate GROMACS version.
Running a GROMACS job on multi node cluster
Here is an example of a submission script GROMACS job on ARC:
#!/bin/bash
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=48
#SBATCH --time=08:00:00
#SBATCH --partition=short
#SBATCH --clusters=arc
module purge
module load GROMACS/2020.4-foss-2020a
mpirun gmx_mpi mdrun -s nsteps800.tpr -deffnm nc2-cubic-md -ntomp 1 -dlb yes -noconfout -npme 64
Also, here is an example of using GROMACS with GPU support on the HTC cluster:
#!/bin/bash
#SBATCH --cluster=htc
#SBATCH --partition=medium
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=5
#SBATCH --mem=377000
#SBATCH --gres=gpu:1
#SBATCH --time=01:00:00
module purge
module load GROMACS/2020.4-fosscuda-2019b
mpirun gmx_mpi mdrun -s nsteps800.tpr -deffnm nc2-cubic-md -ntomp ${SLURM_CPUS_PER_TASK} -dlb yes -noconfout -npme 64