Scalable Software Services for Life Science

GROMACS

About GROMACS

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. Some examples of its usage are described in the use case scenarios.

How to use GROMACS?

If you have never used GROMACS we recommend that you start with the Quick Start guide.

If you are interested in running GROMACS on supercomputers or clusters, HPC usage will help you utilize efficiently such resources.

HPC usage will be valuable to IT personnel and administrators - there you can find information about installation and setup of the program on powerful supercomputers and clusters.

GROMACS is also available as a Grid application and WeNMR has provided several tutorials on the topic.

ScalaLife is providing also cloud images for several stacks.

Software developers may be interested in the Performance section where they can find information on debugging, profiling, analyzing and optimizing the source code. Description of algorithms for high-scalability is also provided in the Performance section.

If you experience problems or have further questions, please search the Forums - they contain a wealth of information. You can also contact us for additional Support.

Please acknowledge the ScalaLife project and Gromacs in your publications following the acknowledgement policy

Happy simulating!