Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics

Thomas C. Bishop, Robert D. Skeel, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

Numerical experiments are performed on a 36,000-atom protein-DNA-water simulation to ascertain the effectiveness of two devices for reducing the time spent computing long-range electrostatics interactions. It is shown for Verlet-I/r-RESPA multiple time stepping, which is based on approximating long-range forces as widely separated impulses, that a long time step of 5 fs results in a dramatic energy drift and that this is reduced by using an even larger long time step. It is also shown that the use of as many as six terms in a fast multipole algorithm approximation to long-range electrostatics still fails to prevent significant energy drift even though four digits of accuracy is obtained.

Original languageEnglish (US)
Pages (from-to)1785-1791
Number of pages7
JournalJournal of Computational Chemistry
Volume18
Issue number14
DOIs
StatePublished - Nov 15 1997

Keywords

  • Fast multipole method
  • Molecular dynamics
  • Multiple time steps
  • r-RESPA
  • Verlet method

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

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