Literature DB >> 20866366

Relative entropy as a universal metric for multiscale errors.

Aviel Chaimovich1, M Scott Shell.   

Abstract

We show that the relative entropy, Srel, suggests a fundamental indicator of the success of multiscale studies, in which coarse-grained (CG) models are linked to first-principles (FP) ones. We demonstrate that Srel inherently measures fluctuations in the differences between CG and FP potential energy landscapes, and develop a theory that tightly and generally links it to errors associated with coarse graining. We consider two simple case studies substantiating these results, and suggest that Srel has important ramifications for evaluating and designing coarse-grained models.

Entities:  

Year:  2010        PMID: 20866366     DOI: 10.1103/PhysRevE.81.060104

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  13 in total

1.  Smoothing protein energy landscapes by integrating folding models with structure prediction.

Authors:  Ari Pritchard-Bell; M Scott Shell
Journal:  Biophys J       Date:  2011-11-01       Impact factor: 4.033

2.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

3.  A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent.

Authors:  Jason A Wagoner; Vijay S Pande
Journal:  J Chem Phys       Date:  2011-06-07       Impact factor: 3.488

4.  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

5.  Communication: Adaptive boundaries in multiscale simulations.

Authors:  Jason A Wagoner; Vijay S Pande
Journal:  J Chem Phys       Date:  2018-04-14       Impact factor: 3.488

6.  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

7.  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

Review 8.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

9.  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

10.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.

Authors:  Jaehyeok Jin; Yining Han; Alexander J Pak; Gregory A Voth
Journal:  J Chem Phys       Date:  2021-01-28       Impact factor: 3.488

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