Parallel molecular dynamics simulation: Implementation of PVM for a lipid membrane

Zhiwu Fang, A. D.J. Haymet, Wataru Shinoda, Susumu Okazaki

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)

Abstract

This paper describes a parallel algorithm for Molecular Dynamics simulation of a lipid membrane using the isothermal-isobaric ensemble. A message-passing paradigm is adopted for interprocessor communications using PVM3 (Parallel Virtual Machine). A data decomposition technique is employed for the parallelization of the calculation of intermolecular forces. The algorithm has been tested both on distributed memory architecture (DEC Alpha 500 workstation clusters) and shared memory architecture (SGI Powerchallenge with 20 R10000 processors) for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer consisting of 32 DPPC molecules and 928 water molecules. For each architecture, we measure the execution time with average work load, and the optimal number of processors for the current simulation. Some dynamical quantities are presented for a 2 ns simulation obtained with 5 processors on DEC Alpha 500 workstations. Our results show that the code is extremely efficient on 5-8 processors, and a useful addition to other major computational resources.

Original languageEnglish
Pages (from-to)295-310
Number of pages16
JournalComputer Physics Communications
Volume116
Issue number2-3
DOIs
Publication statusPublished - 1999
Externally publishedYes

Keywords

  • Lipid simulation
  • Parallel and distributed processing
  • PVM

ASJC Scopus subject areas

  • Hardware and Architecture
  • General Physics and Astronomy

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