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

Abstract

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.

Keywords: Ewald sum local molecular field theory symmetry-preserving mean field theory

Received: 07 May 2015
Revised: 01 July 2015
Accepted manuscript online:

PACS:	02.70.-c	(Computational techniques; simulations)
	05.20.-y	(Classical statistical mechanics)
	47.11.Mn	(Molecular dynamics methods)

Fund:

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.

Corresponding Authors: Hu Zhong-Han
E-mail: zhonghanhu@jlu.edu.cn

Cite this article:

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 2015 Chin. Phys. B 24 120201

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

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