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Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-6363-2521
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2015 (English)In: SoftwareX, ISSN 2352-7110, Vol. 1-2, 19-25 p.Article in journal (Refereed) PublishedText
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, 19-25 p.
Keyword [en]
Free energy, Gpu, Molecular dynamics, Simd
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-181194DOI: 10.1016/j.softx.2015.06.001ScopusID: 2-s2.0-84946416234OAI: oai:DiVA.org:kth-181194DiVA: diva2:900163
Note

Funding Details: 258980, ERC, European Research Council

QC 20160203

Available from: 2016-02-03 Created: 2016-01-29 Last updated: 2016-05-24Bibliographically approved

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Abraham, Mark JamesHess, BerkLindahl, Erik
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Theoretical & Computational BiophysicsScience for Life Laboratory, SciLifeLabKTH
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