Nonbonded Computations

Tamar Schlick

doi:10.1007/978-1-4419-6351-2_10

Nonbonded Computations

Tamar Schlick

Chemistry

Research output: Chapter in Book/Report/Conference proceeding › Chapter

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 language	English (US)
Title of host publication	Interdisciplinary Applied Mathematics
Publisher	Springer Nature
Pages	299-344
Number of pages	46
DOIs	https://doi.org/10.1007/978-1-4419-6351-2_10
State	Published - 2010

Publication series

Name	Interdisciplinary Applied Mathematics
Volume	21
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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10.1007/978-1-4419-6351-2_10

Cite this

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AB - 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.

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KW - Multipole Expansion

KW - Nonbonded Interaction

KW - Spherical Harmonic Function

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Nonbonded Computations

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