Ewald and Multipole Methods for Periodic N Body Problems
 John A. Board Jr.,
 Christopher W. Humphres,
 Christophe G. Lambert,
 William T. Rankin,
 Abdulnour Y. Toukmaji
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Abstract
Many realistic biomolecular simulations require use of periodic boundary conditions to create a surfacefree 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.
 Title
 Ewald and Multipole Methods for Periodic NBody Problems
 Book Title
 Computational Molecular Dynamics: Challenges, Methods, Ideas
 Book Subtitle
 Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21–24, 1997
 Book Part
 Part V
 Pages
 pp 459471
 Copyright
 1999
 DOI
 10.1007/9783642583605_27
 Print ISBN
 9783540632429
 Online ISBN
 9783642583605
 Series Title
 Lecture Notes in Computational Science and Engineering
 Series Volume
 4
 Series ISSN
 14397358
 Publisher
 Springer Berlin Heidelberg
 Copyright Holder
 SpringerVerlag Berlin Heidelberg
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 Editors

 Peter Deuflhard ^{(6)}
 Jan Hermans ^{(7)}
 Benedict Leimkuhler ^{(8)}
 Alan E. Mark ^{(9)}
 Sebastian Reich ^{(10)}
 Robert D. Skeel ^{(11)}
 Editor Affiliations

 6. KonradZuseZentrum Berlin (ZIB)
 7. Department of Biochemistry and Biophysics, University of North Carolina
 8. Department of Mathematics, University of Kansas
 9. Laboratorium für Physikalische Chemie ETH Zentrum
 10. Department of Mathematics and Statistics, University of Surrey
 11. Department of Computer Science, University of Illinois
 Authors

 John A. Board Jr. ^{(12)}
 Christopher W. Humphres ^{(12)}
 Christophe G. Lambert ^{(13)}
 William T. Rankin ^{(12)}
 Abdulnour Y. Toukmaji ^{(12)}
 Author Affiliations

 12. Dept. of Electrical and Computer Engineering, Duke University, Durham, NC, USA
 13. Dept. of Computer Science, Duke University, Durham, NC, USA
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