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用于溶剂化系统分子动力学模拟的弹性袋模型:应用于液态氩

Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid argon.

作者信息

Li Yuhui, Krilov Goran, Berne B J

机构信息

Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA.

出版信息

J Phys Chem B. 2005 Jan 13;109(1):463-70. doi: 10.1021/jp046852t.

Abstract

A new approach is developed to study the dynamics of the localized process in solutions and other condensed phase systems. The approach employs a fluctuating elastic boundary (FEB) model which encloses the simulated system in an elastic bag that mimics the effects of the bulk solvent. This alleviates the need for periodic boundary conditions and allows for a reduction in the number of solvent molecules that need to be included in the simulation. The boundary bag is modeled as a mesh of quasi-particles connected by elastic bonds. The FEB model allows for volume and density fluctuations characteristic of the bulk system, and the shape of the boundary fluctuates during the course of the simulation to adapt to the configuration fluctuations of the explicit solute-solvent system inside. The method is applied to the simulation of a Lennard-Jones model of liquid argon. Various structural and dynamical quantities are computed and compared with those obtained from conventional periodic boundary simulations. The agreement between the two is excellent in most cases, thus validating the viability of the FEB method.

摘要

一种新的方法被开发出来用于研究溶液和其他凝聚相系统中局部过程的动力学。该方法采用了一个波动弹性边界(FEB)模型,该模型将模拟系统封装在一个弹性袋中,以模拟本体溶剂的影响。这减少了对周期性边界条件的需求,并允许减少模拟中需要包含的溶剂分子数量。边界袋被建模为由弹性键连接的准粒子网格。FEB模型允许本体系统的体积和密度波动,并且在模拟过程中边界的形状会波动以适应内部显式溶质-溶剂系统的构型波动。该方法被应用于液态氩的 Lennard-Jones 模型的模拟。计算了各种结构和动力学量,并与从传统周期性边界模拟中获得的量进行了比较。在大多数情况下,两者之间的一致性非常好,从而验证了FEB方法的可行性。

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