Algorithm improvements for molecular dynamics simulations

Per Larsson

doi:10.1002/wcms.3

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Algorithm improvements for molecular dynamics simulations

2011-01-21

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DOI：10.1002/wcms.3

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Abstract

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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. (C) 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 93-108 DOI: 10.1002/wcms.3

Keywords:

ACCESSIBLE SURFACE-AREA

GENERALIZED BORN MODELS

FAST MULTIPOLE METHODS

PARALLEL EVALUATION

NONBONDED FORCE

EFFICIENT

IMPLEMENTATION

APPROXIMATION

CONSTRAINTS

GROMACS

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