GROMACS

GROMACS is a molecular-dynamics and analysis suite. The cluster build is CUDA-enabled.

Load

$ module load md/gromacs

Example (GPU)

A complete production script (scratch, mail, time-limit trap) is in Getting Started. A shorter GPU run:

#!/bin/bash
#SBATCH -J gmx
#SBATCH -c 8
#SBATCH --mem-per-cpu=4G
#SBATCH --gpus=2080ti:1
#SBATCH -t 12:00:00
#SBATCH -o %x-%j.out

module load md/gromacs
WORKDIR="$SCRATCH_DIR/$SLURM_JOB_ID"
mkdir -p "$WORKDIR"
cd "$WORKDIR"
cp "$SLURM_SUBMIT_DIR"/system.tpr .

srun gmx mdrun -nt "$SLURM_CPUS_PER_TASK" -deffnm system
cp -a system.* "$SLURM_SUBMIT_DIR"/

-nt must not exceed the CPUs you reserved. --gpus=1 takes whichever GPU is free; name a type if performance matters.

gmx_mpi is for MPI ranks (#SBATCH -n, still one node). Most GPU runs use thread-MPI gmx as above.

Analysis (gmx rms, gmx energy, …) is lighter but still belongs in a job if it reads large trajectories.