Molecular dynamics on a distributed‐memory multiprocessor

S. L. Lin, J. Mellor‐Crummey, Bernard Pettitt, G. N. Phillips

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.

Original languageEnglish (US)
Pages (from-to)1022-1035
Number of pages14
JournalJournal of Computational Chemistry
Volume13
Issue number8
DOIs
StatePublished - 1992
Externally publishedYes

Fingerprint

Multiprocessor
Molecular Dynamics
Parallelization
Molecular dynamics
Distributed Memory multiprocessors
Data storage equipment
Data structures
Data Structures
Molecular Mechanics
Turnaround time
Molecular mechanics
Communication
Communication Cost
Data Exchange
Electronic data interchange
Parallel Computers
Dynamic Simulation
Equations of motion
Equations of Motion
Simulation

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Molecular dynamics on a distributed‐memory multiprocessor. / Lin, S. L.; Mellor‐Crummey, J.; Pettitt, Bernard; Phillips, G. N.

In: Journal of Computational Chemistry, Vol. 13, No. 8, 1992, p. 1022-1035.

Research output: Contribution to journalArticle

Lin, S. L. ; Mellor‐Crummey, J. ; Pettitt, Bernard ; Phillips, G. N. / Molecular dynamics on a distributed‐memory multiprocessor. In: Journal of Computational Chemistry. 1992 ; Vol. 13, No. 8. pp. 1022-1035.
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