Nonbonded Computations

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Reducing the cost of the nonbonded energy and force computations is of primary importance in molecular mechanics and dynamics simulations of biomolecules. This is because the direct evaluation of these nonbonded interactions involving all atom pairs has the complexity of (formula presented) where N is the number of atoms. Recall that the bonded terms are local and thus have a linear computational complexity; see homework assignment 8 for a related exercise.

Original languageEnglish (US)
Title of host publicationInterdisciplinary Applied Mathematics
PublisherSpringer Nature
Pages299-344
Number of pages46
DOIs
StatePublished - 2010

Publication series

NameInterdisciplinary Applied Mathematics
Volume21
ISSN (Print)0939-6047
ISSN (Electronic)2196-9973

Keywords

  • Brownian Dynamic
  • Fast Multipole Method
  • Multipole Expansion
  • Nonbonded Interaction
  • Spherical Harmonic Function

ASJC Scopus subject areas

  • Applied Mathematics
  • Computational Mathematics
  • Computational Theory and Mathematics
  • Management Science and Operations Research

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