物理化学学报 >> 2011, Vol. 27 >> Issue (08): 1839-1846.doi: 10.3866/PKU.WHXB20110811

理论与计算化学 上一篇    下一篇

基于粗粒化模型对有机溶剂的分子动力学模拟

许佩军1, 唐媛媛1,2, 张静1, 张知博1, 王昆1, 邵颖3, 沈虎峻2, 毛英臣1   

  1. 1. 辽宁师范大学物理与电子技术学院, 辽宁 大连 116029;
    2. 中国科学院大连化学物理研究所, 辽宁 大连 116023;
    3. 大连海事大学物理系, 辽宁 大连 116026
  • 收稿日期:2011-02-28 修回日期:2011-05-09 发布日期:2011-07-19
  • 通讯作者: 沈虎峻, 毛英臣 E-mail:myc@lnnu.edu.cn; hshen@dicp.ac.cn
  • 基金资助:

    中央高校专项资金优秀青年教师基金(2009QN069)资助项目

Molecular Dynamics Simulation of Organic Solvents Based on the Coarse-Grained Model

XU Pei-Jun1, TANG Yuan-Yuan1,2, ZHANG Jing1, ZHANG Zhi-Bo1, WANG Kun1, SHAO Ying3, SHEN Hu-Jun2, MAO Ying-Chen1   

  1. 1. School of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China;
    2. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning Province, P. R. China;
    3. Department of Physics, Dalian Maritime University, Dalian 116026, Liaoning Province, P. R. China
  • Received:2011-02-28 Revised:2011-05-09 Published:2011-07-19
  • Contact: SHEN Hu-Jun, MAO Ying-Chen E-mail:myc@lnnu.edu.cn; hshen@dicp.ac.cn
  • Supported by:

    The project was supported by the Fundamental Research Funds for the Central Universities, China (2009QN069).

摘要:

在基于Boltzmann分布对四种基本构象进行Monte Carlo取样后, 通过与全原子模型的范德华势比较得到了Gay-Berne (GB)参数. 又在对用量化计算得到的分子体系的电势进行电荷、偶极矩和四极矩的拟合后, 得到了电多极展开势(EMP)参数. 利用得到的粗粒化参数, 基于粗粒化模型, 对CHCl3及四氢呋喃(THF)两种有机溶剂进行了分子动力学模拟(MDS), 并将结果同全原子模拟进行了比较. 计算结果表明用粗粒化模型从整体上能重复全原子模型的模拟结果, 但在某些细节的计算与全原子模型有偏差, 其原因可能是目前工作仅考虑了单位点情况, 为此今后在对具有复杂结构的分子进行粗粒化模拟时还应考虑合理放置及增加相互作用位点.

关键词: 粗粒化模型, Gay-Berne势, 电多极展开势, 径向分布函数, 分子动力学模拟

Abstract:

To obtain Gay-Berne (GB) parameters, we carried out Monte Carlo sampling of four reference configurations based on the Boltzmann distribution. After comparing with the van der Waals potential within the all-atom model we obtained the GB parameters. Also by fitting the charge, dipole, and quadrupole with the electric potential obtained from quantum chemical computations with Gaussian 03 we obtained the electric multipole potential (EMP) parameters. With the GB-EMP parameters we then carried out molecular dynamics simulations (MDS) for CHCl3 and tetrahydrofuran (THF) based on the coarse- grained (CG) model. Compared with the all-atom model, the CG model can reproduce the simulation results on the whole, but there are some deviations in the simulations in some details. The reason is that we only take one interaction site into account in this work. Therefore, for more complicated molecules it is necessary to take the placement of the interaction sites into account. Additionally, the multi-sites situation is also considered in the MDS within the frame of the coarse-grained model.

Key words: Coarse-grained model, Gay-Berne potential, Electric multipole potential, Radial distribution function, Molecular dynamics simulation

MSC2000: 

  • O645