Literature DB >> 20701383

A new coarse-grained model for water: the importance of electrostatic interactions.

Zhe Wu1, Qiang Cui, Arun Yethiraj.   

Abstract

A new coarse-grained (CG) model is developed for water. Each CG unit consists of three charged sites, and there is an additional nonelectrostatic soft interaction between central sites on different units. The interactions are chosen to mimic the properties of 4-water clusters in atomistic simulations: the nonelectrostatic component is modeled using a modified Born-Mayer-Huggins potential, and the charges are chosen to reproduce the dipole moment and quadrupole moment tensor of 4-water clusters from atomistic simulations. The parameters are optimized to reproduce experimental data for the compressibility, density, and permittivity of bulk water and the surface tension and interface potential for the air-water interface. This big multipole water (BMW) model represents a qualitative improvement over existing CG water models; for example, it reproduces the dipole potential in membrane-water interface when compared to experiment, with modest additional computational cost as compared to the popular MARTINI CG model.

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Year:  2010        PMID: 20701383     DOI: 10.1021/jp1019763

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  21 in total

Review 1.  Computational studies of peptide-induced membrane pore formation.

Authors:  Richard Lipkin; Themis Lazaridis
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-08-05       Impact factor: 6.237

Review 2.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

Review 3.  SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids.

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Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 4.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 5.  Modeling and simulation of ion channels.

Authors:  Christopher Maffeo; Swati Bhattacharya; Jejoong Yoo; David Wells; Aleksei Aksimentiev
Journal:  Chem Rev       Date:  2012-10-04       Impact factor: 60.622

Review 6.  Recent advances in transferable coarse-grained modeling of proteins.

Authors:  Parimal Kar; Michael Feig
Journal:  Adv Protein Chem Struct Biol       Date:  2014-08-24       Impact factor: 3.507

7.  Coarse-Grained Molecular Models of Water: A Review.

Authors:  Kevin R Hadley; Clare McCabe
Journal:  Mol Simul       Date:  2012-07-04       Impact factor: 2.178

8.  Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains.

Authors:  Wei Han; Klaus Schulten
Journal:  J Chem Theory Comput       Date:  2012-10-11       Impact factor: 6.006

9.  Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Authors:  Lin Shen; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2016-03-15       Impact factor: 6.006

Review 10.  Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.

Authors:  Charlotte I Lynch; Shanlin Rao; Mark S P Sansom
Journal:  Chem Rev       Date:  2020-08-25       Impact factor: 60.622

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