GROMACS

General

• GROMACS home site: 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.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Using GROMACS on ARC

Researchers using GROMACS on ARC are expected to be generally familiar with its capabilities, input file types and their formats and the use of checkpoint files to restart symulations.

Like other calculations on ARC systems, GROMACS is run by submitting an appropriate script for batch scheduling using the sbatch command. For more information about submitting jobs, see Running jobs article.

GROMACS modules

Currently there are several software modules on ARC that provide different versions of GROMACS. The versions differ in the release date as well as in the kind of the CPU architecture the software is compiled for.

You can see them using the module command:

$ module avail gromacs

----------- /global/software/Modules/3.2.10/modulefiles ---------
gromacs/2016.3-gnu
gromacs/2018.0-gnu
gromacs/2019.6-nehalem 
gromacs/2019.6-skylake 
gromacs/5.0.7-gnu