Pittsburgh Supercomputing Center 

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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.

A list of competitive features can be found at http://www.gromacs.org/content/view/12/176.

The calling structure for GROMACS is quite complicated. The examples given below should be considered a guide and not a definitive step-by-step instruction set. 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 at http://www.gromacs.org/Documentation/Tutorials.  See particularly the section "General GROMACS Use". 

Installed on blacklight.

Blacklight Usage

The current version is 5.0.1

To use GROMACS, prepare a job script to:

  1. Load the GROMACS module
    module load gromacs
  2. Run GROMACS procedures

Submit your job script with the qsub command.

Sample Blacklight Script

#PBS -l ncpus=16
#PBS -l walltime=30:00
#PBS -j oe
#PBS -q batch

set echo
source /usr/share/modules/init/csh
#run my executable
module load gromacs
mpirun -np $PBS_NCPUS gmx mdrun -nt $PBS_NCPUS -v -deffnm em