GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, Sweden
SoftwareX, 2015
@article{abraham2015gromacs,
title={GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
author={Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{‘a}ll, Szil{‘a}rd and Smith, Jeremy C and Hess, Berk and Lindahl, Erik},
journal={SoftwareX},
year={2015},
publisher={Elsevier}
}
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.
July 20, 2015 by hgpu
