GROMACS 2018.3

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

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

Accessing the software

To load the module:

$ module load GROMACS/2018.3-foss-2018b

Or, to load the module with GPU support:

$ module load GROMACS/2018.3-fosscuda-2018b

An example command to include in your job script:

$ mpiexec gmx_mpi mdrun -s pr.tpr -deffnm pr

Note the use of the mpiexec command; since this application has been built for parallel execution - this is essential, even for single-core runs.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the GROMACS website for more information regarding this application.


Last modified: 21 December 2018