GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Abstract

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. This work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. Finally, the latest best-in-class compressed trajectory storage format is supported.

Keywords

Affiliated Institutions

• Science for Life Laboratory SE
• University of Tennessee at Knoxville US
• Oak Ridge National Laboratory US
• Stockholm University SE
• KTH Royal Institute of Technology SE

Related Publications