Systematic methods for structurally consistent coarse-grained models

Research output: Chapter in Book/Report/Conference proceedingChapter

39 Citations (Scopus)

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

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Entropy
Mechanics

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Noid, W. G. (2013). Systematic methods for structurally consistent coarse-grained models. In Biomolecular Simulations: Biomolecular Simulations (pp. 487-531). (Methods in Molecular Biology; Vol. 924). Humana Press Inc.. https://doi.org/10.1007/978-1-62703-17-5_19
Noid, W. G. / Systematic methods for structurally consistent coarse-grained models. Biomolecular Simulations: Biomolecular Simulations. Humana Press Inc., 2013. pp. 487-531 (Methods in Molecular Biology).
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Noid, WG 2013, Systematic methods for structurally consistent coarse-grained models. in Biomolecular Simulations: Biomolecular Simulations. Methods in Molecular Biology, vol. 924, Humana Press Inc., pp. 487-531. https://doi.org/10.1007/978-1-62703-17-5_19

Systematic methods for structurally consistent coarse-grained models. / Noid, W. G.

Biomolecular Simulations: Biomolecular Simulations. Humana Press Inc., 2013. p. 487-531 (Methods in Molecular Biology; Vol. 924).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Noid WG. Systematic methods for structurally consistent coarse-grained models. In Biomolecular Simulations: Biomolecular Simulations. Humana Press Inc. 2013. p. 487-531. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-62703-17-5_19