Literature DB >> 22961621

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials.

Peijun Xu1, Hujun Shen, Lu Yang, Yang Ding, Beibei Li, Ying Shao, Yingchen Mao, Guohui Li.   

Abstract

Coarse-grained studies of CH(3)SH, CH(3)CHO and CHCl(3) liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

Entities:  

Year:  2012        PMID： 22961621     DOI： 10.1007/s00894-012-1562-5

Source DB:  PubMed          Journal:  J Mol Model        ISSN： 0948-5023            Impact factor:   1.810


  16 in total

Review 1.  Polarizable force fields.

Authors:  T A Halgren; W Damm
Journal:  Curr Opin Struct Biol       Date:  2001-04       Impact factor: 6.809

Review 2.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

3.  CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

Authors:  Sandeep Patel; Alexander D Mackerell; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-09       Impact factor: 3.376

4.  Distributed Multipole Analysis:  Stability for Large Basis Sets.

Authors:  Anthony J Stone
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

Review 5.  Coarse-grained models for proteins.

Authors:  Valentina Tozzini
Journal:  Curr Opin Struct Biol       Date:  2005-04       Impact factor: 6.809

Review 6.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors:  Eugene Shakhnovich
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

7.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

Authors:  W L Jorgensen; J Tirado-Rives
Journal:  J Am Chem Soc       Date:  1988-03-01       Impact factor: 15.419

8.  Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent.

Authors:  Johnny Wu; Xia Zhen; Hujun Shen; Guohui Li; Pengyu Ren
Journal:  J Chem Phys       Date:  2011-10-21       Impact factor: 3.488

9.  Coarse graining using pretabulated potentials: liquid benzene.

Authors:  Nikolas Zacharopoulos; Niki Vergadou; Doros N Theodorou
Journal:  J Chem Phys       Date:  2005-06-22       Impact factor: 3.488

10.  Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model:  Molecular Dynamics Study of Polyalanine-Based Peptides.

Authors:  Wei Han; Yun-Dong Wu
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006
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  1 in total

1.  An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

Authors:  Hujun Shen; Yan Li; Pengyu Ren; Dinglin Zhang; Guohui Li
Journal:  J Chem Theory Comput       Date:  2014-02-10       Impact factor: 6.006
  1 in total

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