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Caution: this page contains information about the OMNI cluster! There is no corresponding page for the HoRUS cluster.


GROMACS is a software package for molecular dynamics simulation. It is licensed as free and open-source software under the LGPL and can therefore be used for free by anyone on the cluster.

On the OMNI cluster, GROMACS is installed in version 2021.1 (whose user guide can be found here) and 2018.6. If you only type module load gromacs, version 2021.1 is loaded by default. If you want to select the version yourself, you can display the module names with the following command:

$ module avail gromacs
  gromacs/2018.6
  gromacs/2021.1

You can then load a version explicitly with e.g. module load gromacs/2018.6.

Usage

The command to start GROMACS is gmx_mpi. Note that the GROMACS documentation only mentions the gmx command, the two are otherwise identical. You can display an overview of available options with gmx_mpi help. Here is a more detailed list.

Caution: if you run GRAOMACS in an interactive job, you have to specify the MPI version when queuing the job, for example like this: srun --pty --mpi=pmix_v3 gmx_mpi --version

Usage with GPUs

The version 2021.1 also supports usage of GPUs. Please refere to GPU usage for further information.

Aktualisiert um 11:57 am 12. March 2021 von Monika Harlacher