Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems

doi:10.1088/1674-1056/24/12/120201

中国物理B ›› 2015, Vol. 24 ›› Issue (12): 120201-120201.doi: 10.1088/1674-1056/24/12/120201

所属专题： TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics

• TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics • 下一篇

Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems

衣沙沙^{a b}, 潘聪^{a b}, 胡中汉^{a b}

a State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China;
b Institute of Theoretical Chemistry, Jilin University, Changchun 130012, China

收稿日期:2015-05-07 修回日期:2015-07-01 出版日期:2015-12-05 发布日期:2015-12-05
通讯作者: Hu Zhong-Han E-mail:zhonghanhu@jlu.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 91127015 and 21522304) and the Open Project from the State Key Laboratory of Theoretical Physics, and the Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials.

Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems

Yi Sha-Sha (衣沙沙)^{a b}, Pan Cong (潘聪)^{a b}, Hu Zhong-Han (胡中汉)^{a b}

a State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China;
b Institute of Theoretical Chemistry, Jilin University, Changchun 130012, China

Received:2015-05-07 Revised:2015-07-01 Online:2015-12-05 Published:2015-12-05
Contact: Hu Zhong-Han E-mail:zhonghanhu@jlu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 91127015 and 21522304) and the Open Project from the State Key Laboratory of Theoretical Physics, and the Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials.

摘要/Abstract

摘要：

Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the long-ranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules: truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations.

关键词: Ewald sum, local molecular field theory, symmetry-preserving mean field theory

Abstract:

Key words: Ewald sum, local molecular field theory, symmetry-preserving mean field theory

中图分类号: (Computational techniques; simulations)

02.70.-c

05.20.-y (Classical statistical mechanics) 47.11.Mn (Molecular dynamics methods)

衣沙沙, 潘聪, 胡中汉. Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems[J]. 中国物理B, 2015, 24(12): 120201-120201.

Yi Sha-Sha (衣沙沙), Pan Cong (潘聪), Hu Zhong-Han (胡中汉). Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems[J]. Chin. Phys. B, 2015, 24(12): 120201-120201.

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Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems

Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems

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