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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

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

cd ~
mkdir gromacs
cd gromacs
wget http://ftp.gromacs.org/pub/gromacs/gromacs-2023.2.tar.gz
tar xvfz gromacs-2023.2.tar.gz

Load CUDA, Anaconda and MPI modules, 

module load cuda/11.8 anaconda/2023a
module load mpi/openmpi-4.1.5

Create build and install directories, 

mkdir -p 2023.2/build
mkdir 2023.2/install
cd 2023.2/build

Use cmake to configure compiling options, 

cmake ~/gromacs/gromacs-2023.2 -DGMX_MPI=ON -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=~/gromacs/2023.2-gpu

Compile, check and install, 

make
make check
make install

Set up usage environment before running GROMACS programs, 

source ~/gromacs/2023.2/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

This job requests 2 nodes with 4 CPU cores and 2 GPUs per node.

job.sh
#!/bin/bash
#SBATCH --nodes=2              # 2 nodes
#SBATCH --ntasks-per-node=2    # 2 MPI tasks per node
#SBATCH --cpus-per-task=2      # 2 CPU cores per task
#SBATCH --gres=gpu:volta:2     # 2 GPUs per node
#SBATCH --time=01:00:00        # 1 hour


# Load required modules
module load cuda/11.8 mpi/openmpi-4.1.5

# Enable direct GPU to GPU communications
export GMX_ENABLE_DIRECT_GPU_COMM=true

# Activate user install of GROMACS
source ~/gromacs/2023.2-gpu/bin/GMXRC

# Check MPI, GPU and GROMACS
mpirun hostname
nvidia-smi
which gmx_mpi

# Run GROMACS
mpirun gmx_mpi mdrun -s ~/gromacs/bench/benchPEP-h.tpr -ntomp ${SLURM_CPUS_PER_TASK} -pme gpu -update gpu -bonded gpu -npme 1

Finally, submit the job, 

sbatch job.sh

Refer to GROMACS user guide for more info.