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

M AbrahamTheoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, SwedenTeemu J. MurtolaCenter for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-10691 Stockholm, SwedenRoland SchulzDepartment of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, United StatesSzilárd PállTheoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, SwedenJeremy C. SmithDepartment of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, United StatesBerk HessTheoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, 17121 Solna, SwedenErik LindahlCenter for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-10691 Stockholm, Sweden

2015en

ABI

Annotatsiya

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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DOI: 10.1016/j.softx.2015.06.001

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