GROMACS
Gromacs is a free and open-source software suite for high-performance molecular dynamics and output analysis. The software is designed to run either on CPUs or on NVIDIA CUDA-enabled GPUs under a 64-bit Linux operating system.
Installed versions:
Gromacs version 2023.2 (default, recommended)
Gromacs manual can be downloaded from here: https://manual.gromacs.org/
Submitting a Gromacs calculation
This ‘source’ command is needed once per session:
module load gromacs
This commands is equivalent to:
module load gromacs/2023.2-gnu-gpu
The GROMACS SLURM job looks like this:
#!/bin/bash
#SBATCH -A {account}
#SBATCH --job-name={jobname}
#SBATCH --time={0-00:00:00}
#SBATCH --nodes=1
#SBATCH --partition=gpu
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=4
# loading necessary modules
module load gromacs
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
# submintting job
gmx mdrun -v -s {input.tpr} -nsteps 50000 &> run.out
Recommended hardware allocation
Based on our benchmarking on Komondor, we recommend using the GPU-accelerated version of GROMACS for job submissions, with one GPU and 16 CPUs allocated per job.
Last update by Milán SZŐRI: 2025-05-12