Monash University, Faculty of Information Technology, Clayton Campus, Bldg. 63, Wellington Road, Clayton 3800, Australia.
J Comput Chem. 2012 Jun 5;33(15):1364-73. doi: 10.1002/jcc.22967. Epub 2012 Mar 27.
Molecular simulation models are increasingly important tools in efforts to understand the role that water plays in biochemical processes. However, existing models of water have limited capacity to deal with the characteristics of hydrogen bond networks. This article proposes a new fluctuating network (FN) algorithm as an extension of the standard molecular dynamics algorithm. The new algorithm allows for the simulation of a molecular system based on an underlying network, such as the hydrogen bond network in water. This algorithm distinguishes strong from weak network connections, applying a potential that best describes the specific connection behavior. We model liquid water with this new technique using a single-site, isotropic, short-range potential. We successfully reproduce liquid water's signature molecular spacing (as represented by the radial distribution function) and characterize its dynamic properties including the exponential hydrogen bond lifetime distribution, diffusion rate, and average hydrogen bonds per molecule. The FN algorithm allows exploration of the behavior of networked systems where explicit coordination limits are required. As such it could also be used to model covalent interactions, reaction dynamics, and applied to simulation of cellular networks.
分子模拟模型在理解水在生化过程中所起作用的研究中越来越重要。然而，现有的水模型在处理氢键网络的特性方面能力有限。本文提出了一种新的波动网络（FN）算法，作为标准分子动力学算法的扩展。新算法允许根据基础网络（如水中的氢键网络）对分子系统进行模拟。该算法区分强网络连接和弱网络连接，并应用最佳描述特定连接行为的势函数。我们使用这种新技术对液态水进行建模，采用单点各向同性短程势能。我们成功地再现了液态水的特征分子间距（如径向分布函数所表示的），并描述了其动态特性，包括指数型氢键寿命分布、扩散率以及每个分子的平均氢键数。FN 算法允许对需要明确配位限制的网络系统的行为进行探索。因此，它也可以用于模拟共价相互作用、反应动力学，并应用于细胞网络的模拟。
