Paper Info
Title
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions.
Abstract
Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transfer-red between processors by comparison with traditional methods. Specifically, the amount of data transfer-red into and out of a given processor scales as O(R-3/2 p(-1/2)), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice. (c) 2005 Wiley Periodicals, Inc.
Year
DOI
Venue
2005
10.1002/jcc.20267
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
molecular simulation,molecular dynamics,parallel computing,n-body problem,pairwise particle interactions
n-body problem,Pairwise comparison,Computer science,Massively parallel,Parallel computing,Millisecond,Molecular dynamics,Interprocessor communication,Particle,Scalability
Journal
Volume
Issue
ISSN
26
13
0192-8651
Citations 
PageRank 
References 
35
3.47
8
Authors
1
Name
Order
Citations
PageRank
David Elliot Shaw1890139.33