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home > research > biochemistry > gromacs
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GROMACS

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Overview

GROMACS is a versatile package for performing molecular dynamics calculations, i.e. to simulate Newton's equations of motion for systems with hundreds to millions of particles. GROMACS is primarily designed for biochemical molecules like proteins and lipids that have a large number of complicated bonded interactions. GROMACS can also be used for non-biological systems, e.g. polymers.

The HPCx system currently has GROMACS versions 4.0, 3.3.3, 3.3.2, and 3.3.1 installed. The older version 3.2.1 can also be made available on request. New users are strongly recommended to use version 4.0 as this exhibits considerably better scaling than the 3.X versions. Existing users may also wish to migrate to version 4.0. Full details of the changes made to version 4.0 are given here.

A comparison of the performance of version 3.3.2 and version 4.0 for the D.DPPC benchmark is given by following figure:

D.DPPC benchmark for GROMACS versions 3.3.2 and 4.0
(Click for full-size image)

GROMACS 4.0 now scales to at least 512-1024 processors compared with around 32 for version 3.3.2/3.3.3. The SMT (simultaneous multi-threading) results are plotted for the number of virtual processors used, i.e. the 1024 processor result is actually obtained on 512 physical processors.

Accessing GROMACS

HPCx users may access GROMACS. To access this package you should mail the HPCx help desk and we will give you access to the executable.

GROMACS documentation

Copies of the manuals for the different versions can be found here

A number of tutorials for GROMACS can be found here

Further Information

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http://www.hpcx.ac.uk/research/biochemistry/gromacs.html contact email - www@hpcx.ac.uk © UoE HPCX Ltd