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Algorithm improvements for molecular dynamics simulations
Stockholm Univ.
Stockholm Univ.ORCID iD: 0000-0002-7498-7763
Stockholm Univ.ORCID iD: 0000-0002-2734-2794
2011 (English)In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0884, Vol. 1, no 1, 93-108 p.Article in journal (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
Theoretical Chemistry Biophysics
Research subject
SRA - E-Science (SeRC); SRA - Molecular Bioscience
Identifiers
URN: urn:nbn:se:kth:diva-82705DOI: 10.1002/wcms.3ISI: 000295991000009Scopus ID: 2-s2.0-84862813004OAI: oai:DiVA.org:kth-82705DiVA: diva2:498529
Funder
Swedish e‐Science Research Center
Note
QC 20120220Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2012-05-23Bibliographically approved

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Hess, BerkLindahl, Erik

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