The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
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DOI：
10.1063/1.3394862
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发表时间：
2010-04-28
影响因子：
4.4
通讯作者：
Andersen, Hans C.
中科院分区：
文献类型：
--
作者：
Das, Avisek;Andersen, Hans C.
多尺度粗粒化（MS-CG）方法是一种利用从相应原子详细模型的分子动力学模拟获得的数据来确定系统的粗粒化（CG）模型的有效势能函数的方法。MS-CG方法，最初制定的系统在恒定的体积，以前已经给出了严格的统计力学基础的正则系综。在这里，我们提出并测试了一个版本的MS-CG方法适用于等温等压合奏。该方法显示了如何构建一个有效的势能函数的CG系统，产生正确的体积波动，以及正确的分布函数的CG网站的配置空间。该方法的制定需要在CG系统的势能函数中引入明确的体积依赖项。该理论是适用于模拟与各向同性体积波动和情况下，原子和CG模型没有任何分子内的约束，但它是简单的理论扩展到更一般的情况下。目前的理论处理具有短程相互作用的系统。(The使用Ewald方法扩展到库仑力需要额外的考虑）。我们测试的理论恒定压力的MS-CG模拟的一个简单的模型的解决方案。我们表明，无论是体积依赖和坐标依赖的部分的潜在的是转移到更大的系统比一个用来获得这些潜力。(C)2010年美国物理学会。[doi：10.1063/1.3394862]
The multiscale coarse-graining (MS-CG) method is a method for determining the effective potential energy function for a coarse-grained (CG) model of a system using the data obtained from molecular dynamics simulation of the corresponding atomically detailed model. The MS-CG method, as originally formulated for systems at constant volume, has previously been given a rigorous statistical mechanical basis for the canonical ensemble. Here, we propose and test a version of the MS-CG method suitable for the isothermal-isobaric ensemble. The method shows how to construct an effective potential energy function for a CG system that generates the correct volume fluctuations as well as correct distribution functions in the configuration space of the CG sites. The formulation of the method requires introduction of an explicitly volume dependent term in the potential energy function of the CG system. The theory is applicable to simulations with isotropic volume fluctuations and cases where both the atomistic and CG models do not have any intramolecular constraints, but it is straightforward to extend the theory to more general cases. The present theory deals with systems that have short ranged interactions. (The extension to Coulombic forces using Ewald methods requires additional considerations.) We test the theory for constant pressure MS-CG simulations of a simple model of a solution. We show that both the volume dependent and the coordinate dependent parts of the potential are transferable to larger systems than the one used to obtain these potentials. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3394862]