Literature DB >> 20441258

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials.

Luca Larini1, Lanyuan Lu, Gregory A Voth.   

Abstract

Many methodologies have been proposed to build reliable and computationally fast coarse-grained potentials. Typically, these force fields rely on the assumption that the relevant properties of the system under examination can be reproduced using a pairwise decomposition of the effective coarse-grained forces. In this work it is shown that an extension of the multiscale coarse-graining technique can be employed to parameterize a certain class of two-body and three-body force fields from atomistic configurations. The use of explicit three-body potentials greatly improves the results over the more commonly used two-body approximation. The method proposed here is applied to develop accurate one-site coarse-grained water models.

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Year:  2010        PMID: 20441258     DOI: 10.1063/1.3394863

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


  13 in total

1.  Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

Authors:  J W Mullinax; W G Noid
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

2.  Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.

Authors:  Jie Liu; Kannan Sankar; Yuan Wang; Kejue Jia; Robert L Jernigan
Journal:  Biophys J       Date:  2017-04-25       Impact factor: 4.033

3.  Multiscale Multiphysics and Multidomain Models I: Basic Theory.

Authors:  Guo-Wei Wei
Journal:  J Theor Comput Chem       Date:  2013-12       Impact factor: 0.939

Review 4.  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

5.  A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.

Authors:  Anand Srivastava; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

6.  Model reduction of rigid-body molecular dynamics via generalized multipole potentials.

Authors:  Paul N Patrone; Andrew Dienstfrey; G B McFadden
Journal:  Phys Rev E       Date:  2019-12       Impact factor: 2.529

7.  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

8.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.

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

9.  How Water's Properties Are Encoded in Its Molecular Structure and Energies.

Authors:  Emiliano Brini; Christopher J Fennell; Marivi Fernandez-Serra; Barbara Hribar-Lee; Miha Lukšič; Ken A Dill
Journal:  Chem Rev       Date:  2017-09-26       Impact factor: 60.622

Review 10.  Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

Authors:  Gerardo Andrés Cisneros; Kjartan Thor Wikfeldt; Lars Ojamäe; Jibao Lu; Yao Xu; Hedieh Torabifard; Albert P Bartók; Gábor Csányi; Valeria Molinero; Francesco Paesani
Journal:  Chem Rev       Date:  2016-05-17       Impact factor: 60.622

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