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.
How good the scaling is depends on three factors: the speed of the computational part in isolation, the efficiency of the parallel and communication algorithms, and the efficiency of the communication itself. The first two factors we have been optimized extensively. The single processor performance of GROMACS is unrivaled.
Hess et al, GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, J. Chem. Theory Comput.. 2008, 4, 435-447. https://doi.org/10.1021/ct700301q
GROMACS offers analysis of static atomic structures as well as molecular dynamics simulations based on Newton’s equation of motion.
Users at FAU
- Computational Biology (Prof. Rainer Böckmann)
- Computer Chemistry Center (Prof. Tim Clark, Prof. Petra Imhof)
- Bioinformatics (Prof. Heinrich Sticht)
- Institute of Advanced Optical Technologies – Thermophysical Properties (AOT-TP) (Prof. Andreas Fröba)
- Physics Underlying Life Science (PULS) Group (Prof. Ana-Sunčana Smith)
- Lehrstuhl für Pharmazeutische Chemie (Prof. Peter Gmeiner)
Developers at FAU
- no core developers
Tips on Usage at RRZE
- https://doi.org/10.1002/jcc.26011 – More bang for your buck: Improved use of GPU nodes for GROMACS 2018