Literature DB >> 19280011

Effective force coarse-graining.

Yanting Wang1, W G Noid, Pu Liu, Gregory A Voth.   

Abstract

An effective force coarse-graining (EF-CG) method is presented in this paper that complements the more general multiscale coarse-graining (MS-CG) methodology. The EF-CG method determines effective pairwise forces between coarse-grained sites by averaging over the atomistic forces between the corresponding atomic groups in configurations sampled from equilibrium all-atom molecular dynamics simulations. The EF-CG method extracts the transferable part of the MS-CG force field at the cost of reduced accuracy in reproducing certain structural properties. Therefore, the EF-CG method provides an alternative to the MS-CG approach for determining CG force fields that give improved transferability but reduced structural accuracy. The EF-CG method is especially suitable for coarse-graining large molecules with high symmetry, such as bulky organic molecules, and for studying complex phenomena across a range of thermodynamic conditions. The connection between the EF-CG and MS-CG approaches as well as the limitations of the EF-CG method are also discussed. Numerical results for neopentane, methanol and ionic liquid systems illustrate the utility of the method.

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Year:  2009        PMID: 19280011     DOI: 10.1039/b819182d

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  12 in total

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4.  Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study.

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5.  Predicting optical spectra for optoelectronic polymers using coarse-grained models and recurrent neural networks.

Authors:  Lena Simine; Thomas C Allen; Peter J Rossky
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-08       Impact factor: 11.205

6.  Computational Models for the Study of Protein Aggregation.

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Review 7.  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

8.  Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

Authors:  Michael J Quevillon; Jonathan K Whitmer
Journal:  Materials (Basel)       Date:  2018-01-02       Impact factor: 3.623

9.  Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex.

Authors:  Fu-Feng Liu; Bo Huang; Xiao-Yan Dong; Yan Sun
Journal:  PLoS One       Date:  2013-06-12       Impact factor: 3.240

10.  Dynamic prestress in a globular protein.

Authors:  Scott A Edwards; Johannes Wagner; Frauke Gräter
Journal:  PLoS Comput Biol       Date:  2012-05-10       Impact factor: 4.475

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