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

M Abraham | Zendy; Teemu J. Murtola | Zendy; Roland Schulz | Zendy; Szilárd Páll | Zendy; Jeremy C. Smith | Zendy; Berk Hess | Zendy; Erik Lindahl | Zendy

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

Author(s) -

M Abraham,

Teemu J. Murtola,

Roland Schulz,

Szilárd Páll,

Jeremy C. Smith,

Berk Hess,

Erik Lindahl

Publication year - 2015

Publication title -

softwarex

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.528

H-Index - 21

ISSN - 2352-7110

DOI - 10.1016/j.softx.2015.06.001

Subject(s) - computer science , parallelism (grammar) , parallel computing , data parallelism , supercomputer , computer architecture , computational science

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

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