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Algorithm improvements for molecular dynamics simulations
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2011 (English)In: WIRES Computational Molecular Science, ISSN 1759-0876, Vol. 1, no 1, 93-108 p.Article, review/survey (Refereed) Published
Abstract [en]

High-performance implementations of molecular dynamics (MD) simulations play an important role in the study of macromolecules. Recent advances in both hardware and simulation software have extended the accessible time scales significantly, but the more complex algorithms used in many codes today occasionally make it difficult to understand the program flow and data structures without at least some knowledge about the underlying ideas used to improve performance. In this review, we discuss some of the currently most important areas of algorithm improvement to accelerate MD, including floating-point maths, techniques to accelerate nonbonded interactions, and methods to allow multiple or extended time steps. There is also a strong trend of increased parallelization on different levels, including both distributed memory domain decomposition, stream processing algorithms running, e. g., on graphics processing units hardware, and last but not least techniques to decouple simulations to enable massive parallelism on next-generation supercomputers or distributed computing. We describe some of the impacts these algorithms are having in current performance, and also how we believe they can be combined in the future.

Place, publisher, year, edition, pages
2011. Vol. 1, no 1, 93-108 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-67343DOI: 10.1002/wcms.3ISI: 000295991000009OAI: oai:DiVA.org:su-67343DiVA: diva2:470277
Note
authorCount :3Available from: 2011-12-28 Created: 2011-12-28 Last updated: 2011-12-28Bibliographically approved

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