gromacs: Chemical simulation/Molecular dynamics package

Contents

  1. Overview of package
  2. Overview of package
    1. General usage
  3. Availability of package by cluster

Overview of package

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

General usage information

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 of the package gromacs, by cluster

This section lists the available versions of the package gromacson the different clusters.

Available versions of gromacs on the Deepthought2 cluster (RHEL8)

Available versions of gromacs on the Deepthought2 cluster (RHEL8)
Version Module tags CPU(s) optimized for GPU ready?
2019.4 gromacs/2019.4 ivybridge Y
2021 gromacs/2021 ivybridge Y
2018.3 gromacs/2018.3 ivybridge Y

Available versions of gromacs on the Juggernaut cluster

Available versions of gromacs on the Juggernaut cluster
Version Module tags CPU(s) optimized for GPU ready?
2019.4 gromacs/2019.4 x86_64 Y
2018.4 gromacs/2018.4 x86_64 Y

Available versions of gromacs on the Deepthought2 cluster (RHEL6) [DEPRECATED]

Available versions of gromacs on the Deepthought2 cluster (RHEL6) [DEPRECATED]
Version Module tags CPU(s) optimized for GPU ready?
2019.4-plumed
  • 2019.4-plumed
  • (a.k.a gromacs/2019.4-plumed/gnu/9.1.0/openmpi/4.0.1/avx-256/nocuda)
ivybridge N
2018.3-plumed
  • 2018.3-plumed
  • (a.k.a gromacs/2018.3-plumed/gnu/6.1.0/openmpi/1.10.2/avx-256/nocuda)
  • (a.k.a gromacs/2018.3-plumed/gnu/4.9.3/openmpi/1.8.6/avx-256/nocuda)
ivybridge N