Nonbonded Computations

Chapter
Part of the Interdisciplinary Applied Mathematics book series (IAM, volume 21)

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 \(\mathcal{O}({N}^{2})\) 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.

Keywords

Covariance Catalysis Hexagonal Macromolecule Convolution 

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© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Courant Institute of Mathematical Sciences and Department of ChemistryNew York UniversityNew YorkUSA

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