GROMACS

GROMACS#

GROMACS is a molecular dynamics simulation package. For detailed information on using GROMACS, including input files, simulation workflows and command-line options, refer to the official GROMACS documentation.

Available versions#

The following version is available on Calder, with both CPU and GPU builds:

Version	CPU	GPU
`2026.1`	Yes	Yes

Loading GROMACS#

Calder provides CPU and GPU builds of GROMACS. Load the appropriate environment and OpenMPI module before loading GROMACS.

CPU version#

module load calder/cpu openmpi/5.0.10 gromacs/2026.1

GPU version#

module load calder/hopper openmpi/5.0.10 gromacs/2026.1

Note

GROMACS on Calder is built with external MPI support through OpenMPI. Use gmx_mpi to run GROMACS commands; the gmx command will not work with this build.

Example Slurm jobs#

The following examples request one hour of runtime and 16 CPU cores. Adapt the input and output filenames to match your simulation.

CPU job#

Save the following as gromacs_cpu.sh:

#!/bin/bash
#SBATCH --job-name=gromacs-cpu
#SBATCH --time=01:00:00
#SBATCH --ntasks=16
#SBATCH --cpus-per-task=1
#SBATCH --output=gromacs-%j.out
#SBATCH --error=gromacs-%j.err

module load calder/cpu
module load openmpi/5.0.10
module load gromacs/2026.1

export OMP_NUM_THREADS=1

mpirun -np 16 gmx_mpi mdrun -s topol.tpr -deffnm md_cpu

Submit the job with:

sbatch gromacs_cpu.sh

GPU job#

Save the following as gromacs_gpu.sh:

#!/bin/bash
#SBATCH --job-name=gromacs-gpu
#SBATCH --time=01:00:00
#SBATCH --ntasks=2
#SBATCH --partition=calder-gpu-hopper
#SBATCH --gres=gpu:nvidia_h200:2
#SBATCH --output=gromacs-%j.out
#SBATCH --error=gromacs-%j.err

module load calder/hopper
module load openmpi/5.0.10
module load gromacs/2026.1

mpirun -np 2 gmx_mpi mdrun -s topol.tpr -deffnm md_gpu -nb gpu -pme gpu -npme 1 -bonded gpu -v