Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids
✍ Scribed by William S. Young; Charles L. Brooks III
- Publisher
- John Wiley and Sons
- Year
- 1994
- Tongue
- English
- Weight
- 828 KB
- Volume
- 15
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
In this article, we describe a domain decomposition method for the efficient parallel computation of nonbonded forces and energies in condensed-phase molecular systems. This decomposition is based upon the monotonic logical grid (MLG) approach of Boris [J. Boris, 1. Comp. Phys., 66, 1 (1986)l and yields an efficient, scalable algorithm for interparticle interaction computation on private-memory, single-instruction multiple-data (SIMD) parallel computers. We illustrate the application of this technique in a molecular dynamics kernel for rigid molecular solvents by simulating the structural and thermodynamic properties of water and methanol. The performance of this algorithm on the Thinking Machines' CM-2, private-memory SIMD computer, is demonstrated to be good compared to conventional vectoriparallel supercomputers. However, as the fluid becomes less structured performance slightly degrades. 0 1994 by John Wiley & Sons, Inc.
1 . Introduction ince the introduction of numerical methods
S to study the dynamics of atomic and molecular systems on computing machines,' the meth-*Author to whom all correspondence should be addressed. ods of molecular dynamics have become the primary tool for the study of molecular structure, dynamics, and thermodynamics in condensedphase materials.2 This technique has been applied to systems of interest in chemistry, physics, and biophysics. Examples of topics examined are ion ~o l v a t i o n , ~, ~ the characterization of nonnative states of proteins,%' and the interaction of light with bulk solvent.8