A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties
A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties
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DOI：
10.1063/1.4759463
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发表时间：
2012-10-28
影响因子：
4.4
通讯作者：
Leal, L. Gary
中科院分区：
文献类型：
--
作者：
Fu, Chia-Chun;Kulkarni, Pandurang M.;Leal, L. Gary
粗粒化(CG)技术最近引起了人们的极大兴趣，因为它提供了介观分辨率水平的描述，以更少的自由度保持了流体的热力学和输运行为，从而减少了计算工作量。一个基本的问题出现了：一个“自下而上”发展的中尺度模型能在多大程度上很好地恢复分子尺度系统的物理性质？为了回答这个问题，我们系统地探索了CG模式的性质，该模式是为了表示介于原子尺度和连续尺度之间的中间中尺度模式而开发的。这个CG模型旨在降低相对于完全原子模拟的计算成本，并评估在多大程度上可以保留基本参考全原子Lennard-Jones(LJ)系统的热力学和输运性质。在本文中，只详细考虑了热力学性质。输运性质将在后续工作中进行研究。对于粗粒化，我们首先使用迭代Boltzmann逆(IBI)来确定(1-Phi)N中尺度粒子系统的CG势，其中Phi是粗粒化程度，从而再现N原子粒子系统的径向分布函数(RDF)。尽管唯一性定理保证了RDF和有效成对势之间的一对一关系，但我们发现RDF对IBI决定的势的长程部分不敏感，这为进一步匹配其他性质提供了一些显著的灵活性。然后，我们提出了一种IBI的重新公式，作为一种健壮的最小化过程，使得RDF和流体压力能够同时匹配。我们发现，这种新的方法主要改变了CG势的吸引尾区，并改善了相对于纯IBI的等温压缩性。我们还发现，对于CG系统，存在作为Phi的函数的最优相互作用截止长度，这是在保持计算加速比的同时获得足够势能所必需的。为了证明该方法的普适性，我们测试了LJ液体和几种LJ链状液体的一系列状态点。(C)2012年美国物理研究所。[http://dx.doi.org/10.1063/1.4759463]
Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-phi)N mesoscale particle system, where phi is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of phi, that are required to attain an adequate potential while maintaining computational speedup. To demonstrate the universality of the method, we test a range of state points for the LJ liquid as well as several LJ chain fluids. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4759463]