GROMACS

Triton

GROMACS is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen.

How to load Gromacs

To load Gromacs into your computing environment, type in

module load gromacs

This loads Gromacs 2025.1, and its dependencies, into your computing environment.

In order to run calculations with this software, request resources on the compute nodes on t2 by using the following job submission script (set of instructions):

#!/bin/bash

#BSUB -J benchpep_h              # name of your job
#BSUB -e %J.err                  # file name for std. error output
#BSUB -o %J.out                  # file name for std. out output
#BSUB -q normal                  # request run on normal queue
#BSUB -n 1                       # request 1 core
#BSUB -W 2:00                    # request 2 hours of runtime
#BSUB -P XYZ                     # your projectID
#BSUB -gpu "num=1"               # request a single NVIDIA V100 GPU

module load gromacs

gmx_mpi mdrun -v -s benchpep_h.tpr -deffnm benchpep

This job submission script requests resources to run an MD simulation using a single MPI rank mapped to a single NVIDIA V100 GPU on an input file benchpep_h.

Pegasus

Pegasus includes the gromacs/2018.2 module and the gmx executable.

Inspect the installation with:

module avail gromacs
module show gromacs/2018.2

The module automatically loads openmpi-gcc/3.1.1 and cuda/9.1.85. The installed command is gmx; a separate gmx_mpi command is not provided.

Warning

The current GROMACS installation is not usable on the tested Pegasus compute nodes.

LSF tests through the general queue failed before GROMACS could process an input file because libblas.so.3 and liblapack.so.3 were missing from the compute-node environment.

The libraries were present on the login node, but computational GROMACS workloads must not be run there. Contact IDSC support before relying on this module.