Molecular dynamics simulation on the connection machine

A. Windemuth, K. Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

An algorithm for the efficient calculation of macromolecular force fields on the Connection Machine is described. The full force field is separated into bond interactions and non-bonding interactions. Only the latter are implemented on the Connection Machine, the former, less computationally intensive tasks are performed by an existing, conventional molecular dynamics code on the front end. Parallelization of the evaluation of non-bonding interactions is achieved by the Replicated Systolic Loop algorithm introduced in this paper. The algorithm is a variant of the Systolic Loop scheme often used for the computation of 2-particle forces for the classical N-particle problem.

Original languageEnglish (US)
Pages (from-to)353-361
Number of pages9
JournalMolecular Simulation
Volume5
Issue number6
DOIs
StatePublished - Feb 1991

Keywords

  • Connection machine
  • molecular dynamics simulation
  • parallel processing
  • replicated systolic loop algorithm

ASJC Scopus subject areas

  • Chemistry(all)
  • Information Systems
  • Chemical Engineering(all)
  • Modeling and Simulation
  • Materials Science(all)
  • Condensed Matter Physics

Fingerprint

Dive into the research topics of 'Molecular dynamics simulation on the connection machine'. Together they form a unique fingerprint.

Cite this