GROMACS

GROMACS (Groningen Machine for Chemical Simulations) is a versatile package which performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids 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.

Sample scripts for GROMACS use are available in directory /opt/packages/examples/gromacs on Bridges and on Bridges-2.

Documentation

  • GROMACS website
  • GROMACS tutorials
    • The calling structure for GROMACS is quite complicated.  It is strongly recommended that users become familiar with the program before submitting jobs to PSC resources.  A good place to start is the online GROMACS tutorials. See particularly the section “General GROMACS Use”.

Usage on Bridges-2

To see what versions of GROMACS are available and if there is more than one, which is the default, along with some help, type

module spider gromacs

To use GROMACS, include a command like this in your batch script or interactive session to load the GROMACS module: (note ‘module load’ is case-sensitive):

module load gromacs

Usage on Bridges

To see what versions of GROMACS are available type

module avail gromacs

To see what other modules are needed, what commands are available and how to get additional help type

module help  gromacs

To use GROMACS, include a command like this in your batch script or interactive session to load the gromacs module:

module load gromacs

Be sure you also load any other modules needed, as listed by the module help gromacs command.