GROMACS
=======

Gromacs describes itself at http://www.gromacs.org

    GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Running GROMACS on CSD3
-----------------------

GROMACS is supported on each of the hardware partitions on CSD3.

To load the most recent build of GROMACS, first load the partition default environment e.g. (for the `ampere` partition)::

    module purge && module load rhel8/default-amp

and then do::

    module load gromacs

which will make available the gmx_mpi front-end as well as various mdrun binaries.

A sample job script to run GROMACS:

.. literalinclude:: scripts/gromacs/gromacs_cpu_sbatch
    :language: bash
	       
where we have automatically determined the correct `mdrun` binary to run for the slurm partition. This will read from an input file `em.tpr` which can be prepared with the other GROMACS tools.

To run on GPU the job script is almost identical:

.. literalinclude:: scripts/gromacs/gromacs_gpu_sbatch
    :language: bash
		    
where we have modified the directives to slurm to ask for: 1 GPU per node, 4 MPI tasks per GPU, and also loaded the default GPU environment.

Checkpointing GROMACS jobs
--------------------------

In case the simulation requires more than the job timelimits allowed by our policies, GROMACS supports checkpointing. Please refer to the gromacs documentation at https://manual.gromacs.org/current/user-guide/managing-simulations.html.