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Systematic Methods for Structurally Consistent Coarse-Grained Models

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Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 924))

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.

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Acknowledgements

The author gratefully acknowledges the financial support of an NSF CAREER award (NSF Grant No. MCB 1053970) and also start-up funding from the Pennsylvania State University. The author gratefully acknowledges Dr. Navrotskaya for her contributions in developing the present unified approach to systematic coarse-graining and J.W.Mullinax for his contributions in developing the g-YBG theory. WGN also acknowledges the insight and instruction of G. A. Voth, H.C. Andersen, and G. Ayton in many helpful and formative discussions. Finally, WGN gratefully acknowledges Vinod Krishna, Qiang Du, M. Scott Shell, Garegin Papoian, Ard A. Louis, John Weeks, and Matej Praprotnik for many helpful and insightful conversations on the subjects of this work.

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  1. Department of Chemistry, The Pennsylvania State University, University Park, PA, USA

    W. G. Noid

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  1. DSIMB, UMR-S 665, INSERM, rue Alexandre Cabanel 6, Paris, 75015, France

    Luca Monticelli

  2. , Department of Applied Physics, Aalto University, Otakaari, AALTO, FI-00076, Finland

    Emppu Salonen

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Noid, W.G. (2013). Systematic Methods for Structurally Consistent Coarse-Grained Models. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_19

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  • DOI: https://doi.org/10.1007/978-1-62703-017-5_19

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