Systematic methods for structurally consistent coarse-grained models

Research output: Chapter in Book/Report/Conference proceedingChapter

43 Scopus citations

Abstract

This chapter provides a primer on theories for coarse-grained (CG) modeling and, in particular, reviews several systematic methods for determining effective potentials for CG models. The chapter first reviews a statistical mechanics framework for relating atomistic and CG models. This framework naturally leads to a quantitative criterion for CG models that are "consistent" with a particular atomistic model for the same system. This consistency criterion is equivalent to minimizing the relative entropy between the two models. This criterion implies that a many-body PMF is the appropriate potential for a CG model that is consistent with a particular atomistic model. This chapter then presents a unified exposition of the theory and numerical methods for several approaches for approximating this many-body PMF. Finally, this chapter closes with a brief discussion of a few of the outstanding challenges facing the field of systematic coarse-graining.

Original languageEnglish (US)
Title of host publicationBiomolecular Simulations
Subtitle of host publicationBiomolecular Simulations
PublisherHumana Press Inc.
Pages487-531
Number of pages45
ISBN (Print)9781627030168
DOIs
StatePublished - 2013

Publication series

NameMethods in Molecular Biology
Volume924
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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