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Algorithm improvements for molecular dynamics simulations
Author(s) -
Larsson Per,
Hess Berk,
Lindahl Erik
Publication year - 2011
Publication title -
wiley interdisciplinary reviews: computational molecular science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.126
H-Index - 81
eISSN - 1759-0884
pISSN - 1759-0876
DOI - 10.1002/wcms.3
Subject(s) - computer science , molecular dynamics , implementation , software , graphics , domain (mathematical analysis) , parallel computing , graphics processing unit , supercomputer , computational science , decomposition , monte carlo method , parallelism (grammar) , computer graphics , theoretical computer science , artificial intelligence , computer graphics (images) , programming language , computational chemistry , chemistry , mathematics , mathematical analysis , statistics , organic chemistry
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. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 93–108 DOI: 10.1002/wcms.3 This article is categorized under: Structure and Mechanism > Molecular Structures Computer and Information Science > Computer Algorithms and Programming Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods