Handling electrostatic interactions in molecular simulations: A systematic study

被引:14
|
作者
Kolafa, Jiri [3 ]
Moucka, Filip [2 ]
Nezbeda, Ivo [1 ]
机构
[1] Acad Sci Czech Republic, Inst Chem Proc Fundamentals, E Hala Lab Thermodynam, CR-16502 Prague 6, Czech Republic
[2] Univ JE Purkyne, Fac Sci, Usti Nad Labem 40096, Czech Republic
[3] Acad Sci Czech Republic, Inst Chem Proc Fundamentals, Dept Phys Chem, Prague 16628 6, Czech Republic
关键词
molecular simulation; Ewald summation; reaction field; long-range interactions; electrostatic forces;
D O I
10.1135/cccc20080481
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Two qualitatively different models with strong long-range electrostatic interactions, Lennard-Jones diatomics with an embedded dipole moment and TIP4P/ 2005 water, are considered in extensive Monte Carlo and molecular dynamics simulations to systematically study the differences in results caused by different treatments of the long-range electrostatic interactions. In addition to the standard Ewald summation and reaction field methods, we consider also two variants of short-range approximations. Both thermodynamic and structural properties, and both homogeneous and inhomogeneous phases are considered. It is shown that the accuracy of the short-range approximations with carefully selected parameters may be sufficient for a number of applications; however, in some cases one can encounter accuracy limits or structural or other artifacts.
引用
收藏
页码:481 / 506
页数:26
相关论文
共 50 条
  • [31] Study on C-W interactions by molecular dynamics simulations
    Yang, Zhongshi
    Xu, Q.
    Liao, Junqi
    Li, Q.
    Luc, G. -H.
    Luo, G. -N.
    NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS, 2009, 267 (18): : 3144 - 3147
  • [32] An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions
    Lin, Yuchun
    Baumketner, Andrij
    Deng, Shaozhong
    Xu, Zhenli
    Jacobs, Donald
    Cai, Wei
    JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (15):
  • [33] Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions
    Mashimo, Tadaaki
    Fukunishi, Yoshifumi
    Kamiya, Narutoshi
    Takano, Yu
    Fukuda, Ikuo
    Nakamura, Haruki
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9 (12) : 5599 - 5609
  • [34] An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions
    Lin, Yuchun
    Baumketner, Andrij
    Deng, Shaozhong
    Xu, Zhenli
    Jacobs, Donald
    Cai, Wei
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2009, 238
  • [35] A LOCAL REACTION FIELD METHOD FOR FAST EVALUATION OF LONG-RANGE ELECTROSTATIC INTERACTIONS IN MOLECULAR SIMULATIONS
    LEE, FS
    WARSHEL, A
    JOURNAL OF CHEMICAL PHYSICS, 1992, 97 (05): : 3100 - 3107
  • [36] Influence of electrostatic interactions on the properties of cyanobiphenyl liquid crystals predicted from atomistic molecular dynamics simulations
    Wei, Xiaoyu
    Hooper, Justin B.
    Bedrov, Dmitry
    LIQUID CRYSTALS, 2017, 44 (02) : 332 - 347
  • [37] Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study
    Baler, K.
    Martin, O. A.
    Carignano, M. A.
    Ameer, G. A.
    Vila, J. A.
    Szleifer, I.
    JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (04): : 921 - 930
  • [38] Molecular basis for electrostatic interactions in ubiquitin.
    Robertson, AD
    Sundd, M
    Iverson, N
    Kearney, WR
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2002, 223 : C47 - C47
  • [39] The effect of electrostatic boundaries in molecular simulations: symmetry matters
    Pan, Cong
    Yi, Shasha
    Hu, Zhonghan
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2017, 19 (06) : 4861 - 4876
  • [40] Summation of electrostatic interactions in quasi-two-dimensional simulations
    Clark, AT
    Madden, TJ
    Warren, PB
    MOLECULAR PHYSICS, 1996, 87 (05) : 1063 - 1069