Ewald and Multipole Methods for Periodic N-Body Problems

  • John A. BoardJr.
  • Christopher W. Humphres
  • Christophe G. Lambert
  • William T. Rankin
  • Abdulnour Y. Toukmaji
Conference paper

DOI: 10.1007/978-3-642-58360-5_27

Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 4)
Cite this paper as:
Board J.A., Humphres C.W., Lambert C.G., Rankin W.T., Toukmaji A.Y. (1999) Ewald and Multipole Methods for Periodic N-Body Problems. In: Deuflhard P., Hermans J., Leimkuhler B., Mark A.E., Reich S., Skeel R.D. (eds) Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, vol 4. Springer, Berlin, Heidelberg

Abstract

Many realistic biomolecular simulations require use of periodic boundary conditions to create a surface-free environment for the molecule of interest and associated solvent molecules to interact. Electrostatic interactions are the principal computational cost of such simulations. We have implemented two codes: a parallel variant of an Ewald summation method which computes the effect of infinite periodic boundary conditions, and a parallel variant of a multipole algorithm which explicitly computes the interactions within a large but finite periodic system. Each has a regime of applicability, with Ewald favoring smaller systems and fewer processors, and the multipole methods favoring larger systems and more processors. Simulations can now include a full treatment of periodic electrostatics to three or four significant figures of accuracy for a computational cost equivalent to that of a 12Å cutoff simulation.

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Copyright information

© Springer-Verlag Berlin Heidelberg 1999

Authors and Affiliations

  • John A. BoardJr.
    • 1
  • Christopher W. Humphres
    • 1
  • Christophe G. Lambert
    • 2
  • William T. Rankin
    • 1
  • Abdulnour Y. Toukmaji
    • 1
  1. 1.Dept. of Electrical and Computer EngineeringDuke UniversityDurhamUSA
  2. 2.Dept. of Computer ScienceDuke UniversityDurhamUSA

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