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Point-centered domain decomposition for parallel molecular dynamics simulation

delete2000-02-01
delete150
PRE
AI
R
R Koradi
M
Martin Billeter
P
Peter Güntert
DOI：10.1016/S0010-4655(99)00436-1delete
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Abstract

Abstract

En 中文
A new algorithm for molecular dynamics simulations of biological macromolecules on parallel computers, point-centered domain decomposition, is introduced. The molecular system is divided into clusters that are assigned to individual processors, Each cluster is characterized by a center point and comprises all atoms that are closer to its center point than to the center point of any other cluster. The point-centered domain decomposition algorithm is implemented in the new program OPALP using a standard message passing library, so that it runs on both shared memory and massively parallel distributed memory computers. Benchmarks show that the program makes efficient use of up to 100 and more processors for realistic systems of a protein in water comprising 10 000 to 20 000 atoms. (C) 2000 Elsevier Science B.V. All rights reserved.
Keywords:
molecular dynamics
parallel computing
message passing
domain decomposition
MPI
OPALp
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Key information extracted from the uploaded paper, including a brief overview, abstract, background, key highlights, visual analysis, and future outlook.

Journal

Computer Physics Communications cover
Computer Physics Communications
IF:
3.4
Papers:
1.2W
Citations:
3.7W

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