The theory of ultra-coarse-graining. 1. General principles

James F. Dama, Anton V. Sinitskiy, Martin McCullagh, Jonathan Weare, Benoiît Roux, Aaron R. Dinner, Gregory A. Voth

Research output: Contribution to journalArticle

Abstract

Coarse-grained (CG) models provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms correlated over distance scales of many covalent bond lengths and long time scales. Variational methods based on information from simulations of finer-grained (e.g., all-atom) models, for example the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, provide attractive tools for the systematic development of CG models. However, these methods have important drawbacks when used in the "ultra-coarse- grained" (UCG) regime, e.g., at a resolution level coarser or much coarser than one amino acid residue per effective CG particle in proteins. This is due to the possible existence of multiple metastable states "within" the CG sites for a given UCG model configuration. In this work, systematic variational UCG methods are presented that are specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain conclusions of this work connect back to single-state force matching and open up new avenues for method development in that area. These results provide a formal statistical mechanical basis for UCG methods related to force matching and relative entropy CG methods and suggest practical algorithms for constructing optimal approximate UCG models from fine-grained simulation data.

Original languageEnglish (US)
Pages (from-to)2466-2480
Number of pages15
JournalJournal of Chemical Theory and Computation
Volume9
Issue number5
DOIs
StatePublished - May 14 2013

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Entropy
entropy
proteins
Proteins
Atoms
Covalent bonds
covalent bonds
data simulation
Bond length
configurations
metastable state
amino acids
atoms
Amino acids
Amino Acids
optimization
simulation

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Dama, J. F., Sinitskiy, A. V., McCullagh, M., Weare, J., Roux, B., Dinner, A. R., & Voth, G. A. (2013). The theory of ultra-coarse-graining. 1. General principles. Journal of Chemical Theory and Computation, 9(5), 2466-2480. https://doi.org/10.1021/ct4000444

The theory of ultra-coarse-graining. 1. General principles. / Dama, James F.; Sinitskiy, Anton V.; McCullagh, Martin; Weare, Jonathan; Roux, Benoiît; Dinner, Aaron R.; Voth, Gregory A.

In: Journal of Chemical Theory and Computation, Vol. 9, No. 5, 14.05.2013, p. 2466-2480.

Research output: Contribution to journalArticle

Dama, JF, Sinitskiy, AV, McCullagh, M, Weare, J, Roux, B, Dinner, AR & Voth, GA 2013, 'The theory of ultra-coarse-graining. 1. General principles', Journal of Chemical Theory and Computation, vol. 9, no. 5, pp. 2466-2480. https://doi.org/10.1021/ct4000444
Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR et al. The theory of ultra-coarse-graining. 1. General principles. Journal of Chemical Theory and Computation. 2013 May 14;9(5):2466-2480. https://doi.org/10.1021/ct4000444
Dama, James F. ; Sinitskiy, Anton V. ; McCullagh, Martin ; Weare, Jonathan ; Roux, Benoiît ; Dinner, Aaron R. ; Voth, Gregory A. / The theory of ultra-coarse-graining. 1. General principles. In: Journal of Chemical Theory and Computation. 2013 ; Vol. 9, No. 5. pp. 2466-2480.
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