GROMACS
is a software for the simulation of molecular dynamic processes. It is licensed as free and open source software under the LGPL
and can therefore be used free of charge by everyone on the cluster.

GROMACS is installed on the OMNI cluster in versions 2022.1 (whose user guide can be found here
can be found here) and 2018.6 is installed. If you only specify module load gromacs, version 2021.1 is loaded by default. If you want to select the version, you can display the module names with the following command

$ module avail gromacs
  gromacs/2018.6
  gromacs/2022.1

You can then load the corresponding version with module load gromacs/2018.6, for example.

Utilization

The command to start GROMACS is gmx_mpi. Please note that in the GROMACS documentation the command is only called gmx. Otherwise the commands work the same. You can display an overview of possible options with gmx_mpi help. Here
is a more detailed overview.

Attention: If you run GROMACS in an interactive job
you must always specify the MPI version when setting up the job, e.g. srun --pty --mpi=pmix_v3 gmx_mpi --version

Use with GPUs

Version 2022.1 also supports execution on GPUs. All you have to do is follow the information under GPU usage
must be observed.