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

MJ Abraham, T Murtola, R Schulz, S Páll, JC Smith… - SoftwareX, 2015 - Elsevier
SoftwareX, 2015Elsevier
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. These work on every level;
SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of …
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. These 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. The latest best-in-class compressed trajectory storage format is supported.
Elsevier