Generalized verlet algorithm for efficient molecular dynamics simulations with long-range interactions

H. GrubmüLler, H. Heller, A. Windemuth, K. Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

For the purpose of molecular dynamics simulations of large biopolymers we have developed a new method to accelerate the calculation of long-range pair interactions (e.g. Coulomb interaction). The algorithm introduces distance classes to schedule updates of non-bonding interactions and to avoid unnecessary computations of interactions between particles which are far apart. To minimize the error caused by the updating schedule, the Verlet integration scheme has been modified. The results of the method are compared to those of other approximation schemes as well as to results obtained by numerical integration without approximation. For simulation of a protein with 12 637 atoms our approximation scheme yields a reduction of computer time by a factor of seven. The approximation suggested can be implemented on sequential as well as on parallel computers. We describe an implementation on a (Transputer-based) MIMD machine with a systolic ring architecture.

Original languageEnglish (US)
Pages (from-to)121-142
Number of pages22
JournalMolecular Simulation
Volume6
Issue number1-3
DOIs
StatePublished - Mar 1991
Externally publishedYes

ASJC Scopus subject areas

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

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