Development of a Massively Parallel QM/MM Approach Combined with a Theory of Solutions
Development of a Massively Parallel QM/MM Approach Combined with a Theory of Solutions
复制标题
DOI：
10.1007/978-3-319-21626-3_6
复制
发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Hideaki Takahashi;N. Matubayasi
中科院分区：
文献类型：
--
作者：
Hideaki Takahashi;N. Matubayasi
在这篇贡献的文章中，我们回顾了我们的方法，称为QM/MM- er，它将混合QM/MM模拟与能量表示理论相结合。介绍了该方法的最新进展和应用。首先，我们描述了利用实空间网格来表示单电子波函数的QM区域的Kohn-Sham DFT的并行实现。然后，我们的代码在现代并行机上对具有冰结构的大型水簇进行了效率验证。其次，在溶液密度泛函理论的框架内建立了能量表示理论（ER），并给出了其在蛋白质水合作用自由能分析中的应用。第三，我们讨论了QM/MM方法与能量表示方法的耦合，其中由QM溶质的电子密度波动引起的自由能δμ的表达式起着关键作用。作为QM/MM-ER的最新进展，我们开发了一个严格的自由能泛函来计算自由能贡献δμ。描述了该方法的概要以及将其扩展到二阶摄动方法耦合的QM/MM模拟。
In this contributed article we review our method, referred to as QM/MM-ER, which combines the hybrid QM/MM simulation with the theory of energy representation. Our recent developments and applications related to the method are also introduced. First, we describe the parallel implementation of the Kohn-Sham DFT for the QM region that utilizes the real-space grids to represent the one-electron wave functions. Then, the efficiency of our code on a modern parallel machine is demonstrated for a large water cluster with an ice structure. Secondly, the theory of energy representation (ER) is formulated within the framework of the density functional theory of solutions and its application to the free energy analyses of the protein hydration is provided. Thirdly, we discuss the coupling of the QM/MM approach with the method of energy representation, where the formulation for free energyδμdue to the electron density fluctuation of a QM solute plays a key role. As a recent progress in QM/MM-ER we developed a rigorous free energy functional to compute free energy contributionδμ. The outline of the method as well as its extension to the QM/MM simulation coupled with a second-order perturbation approach are described.