A versatile package to perform molecular dynamics.
GROMACS requires an environment module
In order to use GROMACS, you must first load the appropriate environment module:
module load gnu
GROMACS is a powerful and versatile molecular dynamics simulation package. It is capable of solving Newtonian Equations of Motions for extremely large systems that can range in the hundreds of millions of particles. It's primary purpose is for simulating biochemical systems with large numbers of complex bonded interactions such as proteins, lipids and nucleic acids. It is also quite capable of simulating non-biological systems as well since the program can compute such non-bonded interactions extremely quickly.
Use of GROMACS on RCC Resources#
GROMACS is one of the computational chemistry programs available on the HPC cluster. It can be loaded along
with the MPI libraries with
module load gnu openmpi. The MPI Library is required for parallel runs. If you want to run gromacs
serially and/or interactively, you don't need the openmpi module so you can just run
module load gnu. Once these commands are run,
GROMACS commands can be run by prefixing any GROMACS command with
gmx. For example, the
pdb2gmx GROMACS command would be run as
gmx pdb2gmx [options and filenames].
Running Serial GROMACS Jobs on HPC#
To use GROMACS on the HPC, you first need to load the GNU environment module:
Then, GROMACS can be run in serial by using the
gmx commands described in the
GROMACS documentation. For example, to run an energy minimization using molecular
dynamics, see the GROMACS Tutorial for more details, the
following code would be needed:
Running Parallel GROMACS Jobs with MPI#
GROMACS can be run in parallel on multiple nodes using MPI or on multiple cores in a shared memory system using OpenMP. In order to run a parallel job on multiple nodes on RCC Systems, you first must load the gnu and openmpi modules. Then, a parallel job can be executed by using a SLURM script as shown below. For more information on accelerating GROMACS and running it in parallel, please refer to the documentation on that topic and the documentation available on the mdrun command itself.
GROMACS Example SLURM Submit Script#
Save this script in a .sh file. For example, it could be named
TESTJOB.sh.Then, submit this to the
cluster using the following command.