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化学进展 2012, Vol. 24 Issue (06): 1199-1213 前一篇   后一篇

• 量子化学专辑 •

分子模拟中的增强抽样方法

杨立江1, 邵强2, 高毅勤*1   

  1. 1. 北京大学化学与分子工程学院 北京 1000871;
    2. 中国科学院上海药物研究所 上海 201203
  • 收稿日期:2011-11-01 修回日期:2012-02-01 出版日期:2012-06-24 发布日期:2012-05-11
  • 通讯作者: 高毅勤 E-mail:gaoyq@pku.edu.cn
  • 基金资助:

    国家自然科学基金(No. 91027044; 21003004)资助

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Enhanced Sampling Method in Molecular Simulations

Yang Lijiang1, Shao Qiang2, Gao Yiqin1   

  1. 1. College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
    2. Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, China
  • Received:2011-11-01 Revised:2012-02-01 Online:2012-06-24 Published:2012-05-11
分子模拟在化学、物理、生物、材料等多学科的发展中起着越来越重要的作用。然而,受到当前计算机处理速度的限制,分子模拟计算所能够达到的时间尺度同实验或实际应用中要求的时间尺度相比还存在着巨大的差距。增强抽样方法的发展和应用可以有效地拓宽分子模拟所能研究体系的时间尺度,极大地提高分子模拟的热力学和动力学计算能力。本文中先简单介绍增强抽样方法的发展以及几类增强抽样方法的优缺点,然后重点介绍了我们研究组所发展的温度积分抽样方法(Integrated Tempering Sampling, ITS)的基本思路及其在蛋白质折叠研究中的应用。文章最后总结了增强抽样方法发展的新需求,同时也对此研究方向的广阔发展前景进行了展望。
关键词： 分子模拟, 增强抽样, 温度积分抽样, 蛋白质折叠
Molecular simulations play more and more important roles in the studies of chemistry, physics, biology and material sciences, etc. However, due to the limitations of the current computing power, there is still a huge gap between the timescale which can be reached in molecular simulations and that observed in the experiments. Applications of the enhanced sampling method can effectively extend the timescale being approached, so that it improves greatly the thermodynamics and kinetics calculation ability of the molecular simulations. In this paper, the developments and comparisons of the different enhanced sampling methods are introduced briefly, and then the integrated tempering enhanced sampling method (ITS) and its applications to the protein folding simulations are presented in details. At last, the new challenges and prospects in the field of the enhanced sampling methods' development and application are summarized. Contents
1 Introduction
2 Enhanced sampling in the energy and configuration space based on the integrated tempering method
3 Applications: thermodynamics studies of protein folding
4 Future developments
5 Summaries
Key words: molecular simulation, enhanced sampling, integrated tempering sampling, protein folding

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摘要

分子模拟中的增强抽样方法