Literature DB >> 21384955

Coarse-graining errors and numerical optimization using a relative entropy framework.

Aviel Chaimovich1, M Scott Shell.   

Abstract

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.
© 2011 American Institute of Physics.

Entities:  

Year:  2011        PMID: 21384955     DOI: 10.1063/1.3557038

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  24 in total

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4.  Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

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5.  Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion.

Authors:  Timothy C Moore; Christopher R Iacovella; Clare McCabe
Journal:  J Chem Phys       Date:  2014-06-14       Impact factor: 3.488

6.  Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective.

Authors:  Timothy C Moore; Christopher R Iacovella; Anne C Leonhard; Annette L Bunge; Clare McCabe
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7.  Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization.

Authors:  Christopher Arntsen; Chen Chen; Gregory A Voth
Journal:  Chem Phys Lett       Date:  2017-04-22       Impact factor: 2.328

8.  CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.

Authors:  Kiersten M Ruff; Tyler S Harmon; Rohit V Pappu
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

9.  Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data.

Authors:  Chen Chen; Christopher Arntsen; Gregory A Voth
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

10.  Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

Authors:  Sandro Bottaro; Kresten Lindorff-Larsen; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-12-10       Impact factor: 6.006

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