用于密度泛函理论和密度泛函紧束缚的配对相互作用能分解分析以及分子动力学中能量涨落的评估

Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics.

作者信息

Fedorov Dmitri G, Kitaura Kazuo

机构信息

Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST) , Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan.

Advanced Institute for Computational Science (AICS), RIKEN , 7-1-26 Minatojima-Minami-Machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

出版信息

J Phys Chem A. 2018 Feb 15;122(6):1781-1795. doi: 10.1021/acs.jpca.7b12000. Epub 2018 Feb 6.

DOI:10.1021/acs.jpca.7b12000

PMID:29337557

Abstract

Pair interaction energy decomposition analysis in the fragment molecular orbital (FMO) method is extended to treat density functional theory (DFT) and density-functional tight-binding (DFTB). Fluctuations of energy contributions are obtained from molecular dynamics simulations. Interactions at the DFT and DFTB levels are compared to the values obtained with Hartree-Fock, second-order Møller-Plesset (MP2), and coupled cluster methods. Hydrogen bonding in water clusters is analyzed. 200 ps NVT molecular dynamics simulations are performed with FMO for two ligands bound to the Trp-cage miniprotein (PDB 1L2Y ); the fluctuations of fragment energies and interactions are analyzed.

摘要

片段分子轨道（FMO）方法中的成对相互作用能分解分析被扩展用于处理密度泛函理论（DFT）和密度泛函紧束缚（DFTB）。能量贡献的波动通过分子动力学模拟获得。将DFT和DFTB水平的相互作用与通过Hartree-Fock、二阶Møller-Plesset（MP2）和耦合簇方法获得的值进行比较。分析了水簇中的氢键。使用FMO对与色氨酸笼状小蛋白（PDB 1L2Y）结合的两种配体进行了200 ps的NVT分子动力学模拟；分析了片段能量和相互作用的波动。