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.

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

GROMACS calling structure is quite complicated, and it is not recommended that users proceed without at least becoming familiar with the program. The examples should be considered a guide and not a definitive step-by-step instruction set.

Installed on bigben, pople, and salk.

BigBen version

The current version is 3.3.1.

Both double and single precision versions of the mdrun executable, named mdrun_d_xt3 and mdrun_s_xt3, respectively, are available. These are the only executables that run on Bigben's compute nodes. All other GROMACS executables run on the front end nodes.

Example: Simulation of molecular dynamics with a small peptide

To use GROMACS, prepare a job script to:

Load the gromacs module
```
module load gromacs
```
Run GROMACS procedures

Submit your job script with the qsub command.

Pople & Salk version

The current version is 4.0.5

Both double and single precision versions of the mdrun executable, named mdrun_d and mdrun, respectively, are available. The mdrun executables only run on Pople and Salk's compute nodes. All other GROMACS executables run on both the front end nodes and the compute nodes.