Installing and Using GROMACS

GROMACS is a free and open-source software suite for high-performance molecular dynamics and output analysis.

You can learn about GROMACS here: https://www.gromacs.org/.

Install GROMACS with MPI

Select a version on the GROMACS website, then download and extract the tar ball.

cd ~
mkdir gromacs
cd gromacs
wget --no-check-certificate http://ftp.gromacs.org/pub/gromacs/gromacs-2019.6.tar.gz
tar xvfz gromacs-2019.6.tar.gz

Load MPI and Cmake modules,

module load engaging/openmpi/2.0.3 cmake/3.17.3

Create build and install directories,

mkdir -p 2019.6/build
mkdir 2019.6/install
cd 2019.6/build

Use cmake to configure compiling options,

cmake ~/gromacs/gromacs-2019.6 -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=~/gromacs/2019.6/install

Compile, check and install,

make
make check
make install

Set up usage environment,

source ~/gromacs/2019.6/install/bin/GMXRC

Run GROMACS

Firstly, prepare for an input file. Refer to file formats. Here shows an example with an input file named benchPEP-h.tpr downloaded from this page. In these examples we have saved the input files in the ~/gromacs/bench/ directory.

Secondly, create a batch job script, for example, named job.sh.

This job script requests 2 nodes with a total of 8 CPU cores and 50GB of memory.

job.sh

#!/bin/bash
#SBATCH --job-name="production run"
#SBATCH --partition=sched_mit_hill
#SBATCH --constraint=centos7
#SBATCH --mem=50G
#SBATCH -N 2
#SBATCH --ntasks 8
#SBATCH --time=12:00:00


module purge
module load gromacs/2018.4

gmx_mpi=/home/software/gromacs/2018.4/bin/gmx_mpi

if [ -n "$SLURM_CPUS_PER_TASK" ]; then
    ntomp="$SLURM_CPUS_PER_TASK"
else
    ntomp="1"
fi


# setting OMP_NUM_THREADS to the value used for ntomp to avoid complaints from gromacs
export OMP_NUM_THREADS=$ntomp

mpirun -np $SLURM_NTASKS $gmx_mpi mdrun -ntomp $ntomp -deffnm ~/gromacs/bench/benchPEP-h -v

Finally, submit the job,

sbatch job.sh

Refer to GROMACS user guide for more info.