Uppsala Multidisciplinary Center for Advanced Computational Science

GROMACS user guide

This page describes how to run the GROMACS molecular dynamics software on uppmax systems. See the gromacs web page for more information.

Loading the GROMACS module

Load the gromacs module with

module load gromacs

Information about which other modules are loaded will be printed.

Running GROMACS

Versions 4.5.1 to 5.0.4: 

The gromacs tools have been compiled serially. The mdrun program has also been compiled in parallel using MPI. The name of the parallel binary is mdrun_mpi.

Run the parallelized program using:

mpirun -np XXX mdrun_mpi

... where XXX is the number of cores to run the program on.

Version 5.1.1

The binary is gmx_mpi and (e.g.) the mdrun command is issued like this:

mpirun -np XXX gmx_mpi mdrun