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gromacs: Chemical simulation/Molecular dynamics package

Overview of package

Package: gromacs
Description: Chemical simulation/Molecular dynamics package
For more information: http://www.gromacs.org/
Categories: MolecularDynamics
Chemistry
License: OpenSource (LGPL)

General Usage

The GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Starting with Version 2019 the \"g_elpot\" tool for quantifying biomolecular electrostatics from molecular dynamics trajectories is included, too.

This module will add the gmx_mpi and g_elpot commands to your PATH.

The following environmental variables have been defined:

  • $GROMACS_ROOT has been set to the root of the gromacs installation
  • $GROMACS_LIBDIR points to the directory containing the libraries
  • $GROMACS_INCDIR points to the directory containing the header files

You will probably wish to use these by adding the following flags to your compilation command (e.g. to CFLAGS in your Makefile):

  • -I$GROMACS_INCDIR

and the following flags to your link command (e.g. LDFLAGS in your Makefile):

  • -L$GROMACS_LIBDIR -Wl,-rpath,$GROMACS_LIBDIR

Available versions by cluster

This section lists the available versions of the package gromacson the UMD HPC clusters.

Versions available on the Zaratan cluster

Version Module tags CPU(s) optimized for GPU ready?
2021.4 2021.4 zen2 Yes
2018.4 2018.4 zen Yes
2023 2023 icelake, zen2 Yes
2019.4 2019.4 zen Yes