GROMACS

GROMACS (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics

GROMACS (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.)

Licensing Terms and Conditions

GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see GROMACS Homepage for details).

How to run on Merlin7

2025.2

CPU nodes

module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-ax23-A100-gpu gromacs/2025.2-whcq-omp

A100 nodes

module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-3vzj-A100-gpu gromacs/2025.2-vbj4-A100-gpu-omp

GH nodes

module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-blxc-GH200-gpu gromacs/2025.2-cjnq-GH200-gpu-omp

2025.3

CPU nodes

module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-n4yf-A100-gpu gromacs/2025.3-6ken-omp

A100 nodes

module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-xqhy-A100-gpu gromacs/2025.3-ohlj-A100-gpu-omp

GH nodes

module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-inxi-GH200-gpu gromacs/2025.3-yqlu-GH200-gpu-omp

SBATCH CPU, 4 MPI ranks, 16 OMP threads

#!/bin/bash
#SBATCH --time=00:10:00      # maximum execution time of 10 minutes
#SBATCH --nodes=1            # requesting 1 compute node
#SBATCH --ntasks=4           # use 4 MPI rank (task)
#SBATCH --partition=hourly
#SBATCH --cpus-per-task=16 # modify this number of CPU cores per MPI task
#SBATCH --output=_scheduler-stdout.txt
#SBATCH --error=_scheduler-stderr.txt

unset PMODULES_ENV
module purge
module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-ax23-A100-gpu gromacs/2025.2-whcq-omp

export FI_CXI_RX_MATCH_MODE=software

# Add your input (tpr) file in the command below
srun gmx_mpi grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx
srun gmx_mpi mdrun -s step6.0_minimization.tpr -pin on -ntomp ${SLURM_CPUS_PER_TASK}

SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks

#!/bin/bash
#SBATCH --time=00:10:00      # maximum execution time of 10 minutes
#SBATCH --output=_scheduler-stdout.txt
#SBATCH --error=_scheduler-stderr.txt
#SBATCH --nodes=1             # number of GH200 nodes with each node having 4 CPU+GPU
#SBATCH --ntasks-per-node=4  # 4 MPI ranks per node
#SBATCH --cpus-per-task=16    # 16 OMP threads per MPI rank
#SBATCH --cluster=gmerlin7
#SBATCH --hint=nomultithread
#SBATCH --partition=a100-hourly
#SBATCH --gpus=4

unset PMODULES_ENV
module purge
module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-3vzj-A100-gpu gromacs/2025.2-vbj4-A100-gpu-omp

export FI_CXI_RX_MATCH_MODE=software

export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true
export GMX_FORCE_UPDATE_DEFAULT_GPU=true
export GMX_ENABLE_DIRECT_GPU_COMM=1
export GMX_FORCE_GPU_AWARE_MPI=1

# Add your input (tpr) file in the command below
srun gmx_mpi grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx
srun gmx_mpi mdrun -s step6.0_minimization.tpr -ntomp ${SLURM_CPUS_PER_TASK}

SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks

#!/bin/bash
#SBATCH --time=00:10:00      # maximum execution time of 10 minutes
#SBATCH --output=_scheduler-stdout.txt
#SBATCH --error=_scheduler-stderr.txt
#SBATCH --nodes=1             # number of GH200 nodes with each node having 4 CPU+GPU
#SBATCH --ntasks-per-node=2  # 2 MPI ranks per node
#SBATCH --cpus-per-task=18    # 18 OMP threads per MPI rank
#SBATCH --cluster=gmerlin7
#SBATCH --hint=nomultithread
#SBATCH --partition=gh-hourly
#SBATCH --gpus=2

unset PMODULES_ENV
module purge
module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-blxc-GH200-gpu gromacs/2025.2-cjnq-GH200-gpu-omp

export FI_CXI_RX_MATCH_MODE=software

export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true
export GMX_FORCE_UPDATE_DEFAULT_GPU=true
export GMX_ENABLE_DIRECT_GPU_COMM=1
export GMX_FORCE_GPU_AWARE_MPI=1

# Add your input (tpr) file in the command below
srun gmx_mpi grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx
srun gmx_mpi mdrun -s step6.0_minimization.tpr -ntomp ${SLURM_CPUS_PER_TASK}

Developing your own GPU code

A100

module purge
module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-3vzj-A100-gpu gromacs/2025.2-vbj4-A100-gpu-omp cmake/3.31.6-o3lb python/3.13.1-cyro

git clone https://github.com/gromacs/gromacs.git
cd gromacs

mkdir build && cd build
cmake -DCMAKE_C_COMPILER=gcc-12 \
    -DCMAKE_CXX_COMPILER=g++-12 \
    -DGMX_MPI=on \
    -DGMX_GPU=CUDA \
    -GMX_CUDA_TARGET_SM="80" \ # 90 for the Hopper GPUs
    -DGMX_DOUBLE=off \ # turn on double precision only if useful
    ..

make