Literature DB >> 27448876

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation.

Tanmoy Sanyal1, M Scott Shell1.   

Abstract

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Entities:  

Year:  2016        PMID: 27448876     DOI: 10.1063/1.4958629

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


  7 in total

Review 1.  Advances in coarse-grained modeling of macromolecular complexes.

Authors:  Alexander J Pak; Gregory A Voth
Journal:  Curr Opin Struct Biol       Date:  2018-11-30       Impact factor: 6.809

Review 2.  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

3.  Best Practices for Foundations in Molecular Simulations [Article v1.0].

Authors:  Efrem Braun; Justin Gilmer; Heather B Mayes; David L Mobley; Jacob I Monroe; Samarjeet Prasad; Daniel M Zuckerman
Journal:  Living J Comput Mol Sci       Date:  2018-11-29

4.  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

Review 5.  Role of Entropy in Colloidal Self-Assembly.

Authors:  Brunno C Rocha; Sanjib Paul; Harish Vashisth
Journal:  Entropy (Basel)       Date:  2020-08-10       Impact factor: 2.524

6.  Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites.

Authors:  Alexander J Pak; Thomas Dannenhoffer-Lafage; Jesper J Madsen; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2019-02-15       Impact factor: 6.006

7.  Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.

Authors:  Adam Liwo; Cezary Czaplewski; Adam K Sieradzan; Agnieszka G Lipska; Sergey A Samsonov; Rajesh K Murarka
Journal:  Biomolecules       Date:  2021-09-11
  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.