Gromacs

Overview

GROMACS is a molecular dynamics package developed at the University of Groningen Chemistry department.

Some features of the GROMACS software:

• Standard Molecular Dynamics simulations
• Energy minimizations
• High performance due to well optimized code and smart algorithms
• Automatic topology generation from a building block library
• Flexible force field usage
• Non-Equilibrium Molecular Dynamics

Version 3.2.1 of Gromacs is installed on the CSAR systems.

Restrictions on Use

There are no restrictions on using the Gromacs software.

Set Up Procedure

In order to run Gromacs you should load the gromacs module by typing module load gromacs

Running the Code

On Newton, the executables for GROMACS are located in /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin. You should add this to your path in order to use them. All of the programs except mdrun are designed to be run in serial mode - you can run them interactively or via the batch system. The mdrun executable must be started using mpirun, and must be run via the batch system. For example, for a 64 processor simulation you would add:

mpirun -np 64 /usr/local/apps/supported/gromacs/ia64-unknown-linux-gnu/bin/mdrun

to your batch submission script.

Both the single and double precision versions of the executables are available on Newton. The double precision versions are suffixed with _d for example:

mdrun_d

For more details of how to run MPI applications on the different CSAR machines please see the submitting jobs web page.

Further Information

Please visit the GROMACS Web Pages for further information.