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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics, Theoretical Biological Physics.ORCID iD: 0000-0001-6363-2521
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics, Theoretical Biological Physics.ORCID iD: 0000-0003-0603-5514
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2015 (English)In: SoftwareX, E-ISSN 2352-7110, Vol. 1-2, p. 19-25Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2015. Vol. 1-2, p. 19-25
Keywords [en]
Molecular dynamics, GPU, SIMD, Free energy
National Category
Physical Sciences
Research subject
Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-248468DOI: 10.1016/j.softx.2015.06.001Scopus ID: 2-s2.0-84946416234OAI: oai:DiVA.org:kth-248468DiVA, id: diva2:1303357
Note

QC 20190429

Available from: 2019-04-09 Created: 2019-04-09 Last updated: 2019-04-29Bibliographically approved

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fulltext(1990 kB)22 downloads
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Publisher's full textScopushttp://www.sciencedirect.com/science/article/pii/S2352711015000059

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