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一种简单、高效的可极化粗粒化水分子动力学模拟模型。

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

机构信息

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland.

出版信息

J Chem Phys. 2011 Feb 28;134(8):084110. doi: 10.1063/1.3553378.

Abstract

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

摘要

开发能够正确表示化合物重要特征的粗粒化 (CG) 模型对于克服目前原子分子动力学模拟中时间尺度和系统规模的限制至关重要。文献中报道的大多数方法将一个或多个分子建模为单个不带电的 CG 珠。然而,对于水,这种对静电相互作用的隐式处理未能模拟重要性质,例如介电屏蔽。因此,提出了一种粗粒化模型来处理水分子簇之间的静电相互作用。五个水分子嵌入由两个带相反电荷的粒子组成的球形 CG 珠中,这些粒子代表偶极子。连接珠中两个粒子的键不受约束,这使得模型具有极化能力。使用室温下液态水的实验和全原子模拟数据对模型进行参数化。实验密度和相对静态介电常数被选为主要目标性质。将模型性质与实验、适当大小的液相简单点电荷水分子簇以及其他 CG 水模型(如果有的话)获得的性质进行比较。比较表明,CG 模型不能再现所有原子性质,因此在进行粗粒化时必须选择关键性质。然而,CG 模型再现了液态水的关键特征,同时计算效率比标准的细粒度原子水模型高 1-2 个数量级。

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