Accelerated molecular dynamics simulation with the parallel fast multipole algorithm

John A. Board, Jeffrey W. Causey, James F. Leathrum, Andreas Windemuth, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

We have implemented the fast multipole algorithm (FMA) of Greengard and Rokhlin and incorporated it into the molecular dynamics program MD of Windemuth and Schulten, allowing rapid computation of the non-bonded forces acting in dynamical protein systems without truncation or other corruption of the Coulomb force. The resulting program speeds up simulations of protein systems with approximately 24000 atoms by up to an order of magnitude on a single workstation. Additionally, we have implemented a parallel version of the three-dimensional FMA code on a loosely coupled workstations, further reducing simulation times. Large (in both size of system and length of simulated time) protein molecular dynamics simulations are now possible on workstations rather than supercomputers, and very large protein computations are possible on clusters of workstations and parallel machines.

Original languageEnglish (US)
Pages (from-to)89-94
Number of pages6
JournalChemical Physics Letters
Volume198
Issue number1-2
DOIs
StatePublished - Oct 2 1992

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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