GROMACS 2026.1 Usage Guide

General Information

GROMACS is a high-performance molecular dynamics (MD) software designed for biomolecular simulations.

It is optimized for:

• MPI parallelism
• OpenMP threading
• SIMD vectorization (AVX)

On Performetrica HPC:

• MPI: OpenMPI 5.0.3
• OpenMP: Enabled (max 128 threads)
• FFT: FFTW 3.3.10

Executable path: /perf/papps/GROMACS/2026.1-gompi-2024a/bin/gmx_mpi

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Load Module

ml GROMACS/2026.1-gompi

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Verify Installation

gmx --version
gmx_mpi --version

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Build Details

• Version: 2026.1
• Precision: Mixed
• Memory model: 64-bit
• SIMD: AVX_256
• Compiler: GCC 13.3.0
• MPI: OpenMPI 5.0.3
• OpenMP: Enabled (max 128 threads)
• GPU: Disabled
• FFT: FFTW 3.3.10 (CPU)
• PLUMED: Enabled
• Colvars: Enabled

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Running Modes

Hybrid MPI + OpenMP

gmx_mpi mdrun -ntmpi 4 -ntomp 4 -s topol.tpr

OpenMP only

gmx mdrun -ntomp 8 -s topol.tpr

MPI only

gmx_mpi mdrun -ntmpi 16 -ntomp 1 -s topol.tpr

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Slurm Example

#!/bin/bash
#SBATCH -J gromacs_job
#SBATCH -p defq
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
#SBATCH --time=04:00:00
#SBATCH --output=%x_%j.out
#SBATCH --error=%x_%j.err
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=your_email@example.com

ml GROMACS/2026.1-gompi

export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}

echo "Job started on $(hostname)"
echo "Node list: $SLURM_JOB_NODELIST"
echo "Start time: $(date)"

srun gmx_mpi mdrun -ntomp ${OMP_NUM_THREADS} -s topol.tpr -deffnm md

echo "End time: $(date)"

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Performance Tips

• Ensure ntmpi × ntomp = total cores
• Start with small tests
• Avoid over-allocation
• Use hybrid mode for best performance
• Monitor with squeue

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Logs

grep Performance *.log

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Notes

• GPU support is disabled on this build
• Do not run on login nodes