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GROMACS

GROMACS on Perun

GROMACS is a versatile package to perform molecular dynamics 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 it can also be used for dynamics of non-biological systems, such as polymers and fluid dynamics.

User Guide

Available Versions

Following versions of GROMACS are currently available:

  • Runtime dependencies:
    • None, required libraries and dependencies are loaded automatically with the GROMACS/2025.3-foss-2025b module.

You can load the GROMACS module by following command: 

GROMACS/2025.3-foss-2025b

Example Run Script

You can copy and modify this script to gromacs_run.sh and submit job to a compute node by command sbatch gromacs_run.sh.


#!/bin/bash
#SBATCH --job-name=                     # Name of the job
#SBATCH --account=                      # Project account number
#SBATCH --partition=                    # Partition name (cpu_short, cpu_long, cpu_hm_short, cpu_hm_long)
#SBATCH --nodes=                        # Number of nodes
#SBATCH --ntasks=                       # Total number of MPI ranks
#SBATCH --cpus-per-task=                # Number of threads per MPI rank
#SBATCH --time=hh:mm:ss                 # Time limit (hh:mm:ss)
#SBATCH --output=stdout.%j.out          # Standard output (%j = Job ID)
#SBATCH --error=stderr.%j.err           # Standard error
#SBATCH --mail-type=END,FAIL            # Notifications for job done or failed
#SBATCH --mail-user=                    # Email address for notifications

# === Metadata functions ===
log_job_start() {
    echo "================== SLURM JOB METADATA =================="
    printf " Job ID        : %s\n" "$SLURM_JOB_ID"
    printf " Job Name      : %s\n" "$SLURM_JOB_NAME"
    printf " Partition     : %s\n" "$SLURM_JOB_PARTITION"
    printf " Nodes         : %s\n" "$SLURM_JOB_NUM_NODES"
    printf " Tasks (MPI)   : %s\n" "$SLURM_NTASKS"
    printf " CPUs per Task : %s\n" "$SLURM_CPUS_PER_TASK"
    printf " Account       : %s\n" "$SLURM_JOB_ACCOUNT"
    printf " Submit Dir    : %s\n" "$SLURM_SUBMIT_DIR"
    printf " Work Dir      : %s\n" "$PWD"
    printf " Start Time    : %s\n" "$(date)"
    echo "========================================================"
}

log_job_end() {
    printf " End Time      : %s\n" "$(date)" 
    echo "========================================================"
}

# === Load required module(s) ===
module purge
module load GROMACS/2025.3-foss-2025b

# === Set working directories ===
# Use shared filesystems for cross-node calculations
INIT_DIR="${SLURM_SUBMIT_DIR}"
WORK_DIR="/work/${SLURM_JOB_ACCOUNT}/${SLURM_JOB_ID}"
mkdir -p "$WORK_DIR"

# === Input/output file declarations ===
INPUT_FILES=""                          # Adjust as needed
OUTPUT_FILES=""                         # Adjust as needed

# === Copy input files to scratch ===
cp $INPUT_FILES "$WORK_DIR"

# === Change to working directory ===
cd "$WORK_DIR" || { echo "Failed to cd into $WORK_DIR"; exit 1; }

log_job_start >> "$INIT_DIR/jobinfo.$SLURM_JOB_ID.log"

# === Run GROMACS ===
mpiexec -np ${SLURM_NTASKS} gmx_mpi mdrun -ntomp ${SLURM_CPUS_PER_TASK} ...

# === Copy output files back ===
cp $OUTPUT_FILES "$INIT_DIR"

# === Optional: clean up scratch ===
# rm -rf "$WORK_DIR"

log_job_end >> "$INIT_DIR/jobinfo.$SLURM_JOB_ID.log"
Created by: Marek Štekláč