Literature DB >> 18688358

A transferable coarse-grained model for hydrogen-bonding liquids.

Pavel A Golubkov1, Johnny C Wu, Pengyu Ren.   

Abstract

We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations.

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Year:  2008        PMID: 18688358      PMCID: PMC2443098          DOI: 10.1039/b715841f

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


  11 in total

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3.  Molecular structure of alcohol-water mixtures.

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Review 5.  Biomolecular modeling: Goals, problems, perspectives.

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6.  Coarse-grained simulation of amphiphilic self-assembly.

Authors:  David J Michel; Douglas J Cleaver
Journal:  J Chem Phys       Date:  2007-01-21       Impact factor: 3.488

7.  Generalized coarse-grained model based on point multipole and Gay-Berne potentials.

Authors:  Pavel A Golubkov; Pengyu Ren
Journal:  J Chem Phys       Date:  2006-08-14       Impact factor: 3.488

8.  Modeling real dynamics in the coarse-grained representation of condensed phase systems.

Authors:  Sergei Izvekov; Gregory A Voth
Journal:  J Chem Phys       Date:  2006-10-21       Impact factor: 3.488

9.  Molecular segregation observed in a concentrated alcohol-water solution.

Authors:  S Dixit; J Crain; W C K Poon; J L Finney; A K Soper
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10.  Molecular dynamics simulation study on the phase behavior of the Gay-Berne model with a terminal dipole and a flexible tail.

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Journal:  J Chem Phys       Date:  2004-04-22       Impact factor: 3.488

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  10 in total

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3.  Coarse-grained model for simulation of RNA three-dimensional structures.

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4.  Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

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Authors:  Johnny Wu; Xia Zhen; Hujun Shen; Guohui Li; Pengyu Ren
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Review 6.  Bottom-up Coarse-Graining: Principles and Perspectives.

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7.  United polarizable multipole water model for molecular mechanics simulation.

Authors:  Rui Qi; Lee-Ping Wang; Qiantao Wang; Vijay S Pande; Pengyu Ren
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8.  Conformational preference of ChaK1 binding peptides: a molecular dynamics study.

Authors:  Jiajing Zhang; Christopher A King; Kevin Dalby; Pengyu Ren
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9.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.

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10.  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

  10 in total

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