Exploiting the parallelisation inherent in the windowing approach to Monte Carlo energy perturbation calculations

Jonathan D. Wright, Christopher A. Reynolds

Research output: Contribution to journalArticle

Abstract

A parallel version of a Monte Carlo free energy difference code has been implemented to exploit the potential for parallelisation inherent in the free energy perturbation windowing procedure. Since all the windows are run in parallel, the major overhead compared with the serial implementation is the requirement to increase the equilibration for each window from 106 configurations to 3 × 106 configurations (106 configurations were used for data collection for each window). For the perturbation of nitroimidazoles to their radical anions in a box of 500 water molecules, the parallel code gives essentially identical free energy of hydration differences to the serial code. The 64 processor CRAY T3D version of the code has an execution overhead of only 25% compared with the single processor version, suggesting that this approach has great potential. In particular, the approach could be combined with approaches to parallelise the non-bonded interactions, permitting parallelisation over several thousand processors.

Original languageEnglish
Pages (from-to)131-135
Number of pages5
JournalJournal of Molecular Structure: THEOCHEM
Volume427
Issue number1-3
DOIs
Publication statusPublished - 16 Mar 1998
Externally publishedYes

Keywords

  • Free energy perturbation
  • Hydration
  • Monte Carlo
  • Nitroimidazole
  • Parallelisation

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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