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Gromacs

Overview

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

Core Methods

GROMACS offers analysis of static atomic structures as well as molecular dynamics simulations based on Newton’s equation of motion.

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Further Information