Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

JOURNAL OF COMPUTATIONAL PHYSICS

卷:245

Article

Deng, Shaozhong¹  Xue, Changfeng²  Baumketner, Andriy³  Jacobs, Donald³  Cai, Wei¹ 

[1] Univ N Carolina, Dept Math & Stat, Charlotte, NC 28223 USA

[2] Yancheng Inst Technol, Dept Fundamental Sci, Yancheng 224051, Jiangsu, Peoples R China

[3] Univ N Carolina, Dept Phys & Opt Sci, Charlotte, NC 28223 USA

关键词: Method of images;    Reaction field;    Electrostatic interaction;    Hybrid explicit/implicit solvation model;   

DOI  :  10.1016/j.jcp.2013.03.027

来源: Elsevier

【 摘 要 】

This paper extends the image charge solvation model (ICSM) [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. (C) 2013 Elsevier Inc. All rights reserved.

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