Combining Linear-Scaling DFT with Subsystem DFT in Born Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution
Combining Linear-Scaling DFT with Subsystem DFT in Born Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution
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DOI：
10.1021/acs.jctc.6b00398
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发表时间：
2016-07-01
影响因子：
5.5
通讯作者：
VandeVondele, Joost
中科院分区：
文献类型：
--
作者：
Andermatt, Samuel;Cha, Jinwoong;VandeVondele, Joost
在这项工作中，嵌入在分子环境中的大型系统的有效模拟方法。这些方法联合收割机了线性标度（LS）KohnSham（KS）密度泛函理论（DFT）和子系统（SS）DFT。LS DFT对于大的子系统是有效的，而SS DFT对于大的小分子集合是具有较小前因子的线性标度。SS和LS的组合，这是一种嵌入方法，可以导致10倍的加速比纯LS模拟水溶液中的大型系统。除了一个基态BornOppenheimer SS+LS实现，一个依赖于时间的密度泛函理论为基础的Escherichfest分子动力学（EMD）使用密度矩阵传播，允许执行非绝热动力学。密度矩阵为基础的EMD在SS框架是自然的线性标度，并出现适合于研究在溶液中的分子的电子动力学。在LS框架中，只要密度矩阵在时间传播期间保持稀疏，就产生线性缩放。然而，我们通常会发现一个小于指数衰减的密度矩阵后，足够长的EMD运行，防止LS EMD模拟任意精度。这些方法在各种系统上进行了测试，包括染料光谱，TiO 2纳米颗粒的电子结构，碳纳米管中的电子传输，以及明确解决方案中的卫星烟草花叶病毒。
In this work, methods for the efficient simulation of large systems embedded in a molecular environment are presented. These methods combine linear-scaling (LS) KohnSham (KS) density functional theory (DFT) with subsystem (SS) DFT. LS DFT is efficient for large subsystems, while SS DFT is linear scaling with a smaller prefactor for large sets of small molecules. The combination of SS and LS, which is an embedding approach, can result in a 10-fold speedup over a pure LS simulation for large systems in aqueous solution. In addition to a ground-state BornOppenheimer SS+LS implementation, a time-dependent density functional theory-based Ehrenfest molecular dynamics (EMD) using density matrix propagation is presented that allows for performing nonadiabatic dynamics. Density matrix-based EMD in the SS framework is naturally linear scaling and appears suitable to study the electronic dynamics of molecules in solution. In the LS framework, linear scaling results as long as the density matrix remains sparse during time propagation. However, we generally find a less than exponential decay of the density matrix after a sufficiently long EMD run, preventing LS EMD simulations with arbitrary accuracy. The methods are tested on various systems, including spectroscopy on dyes, the electronic structure of TiO2 nanoparticles, electronic transport in carbon nanotubes, and the satellite tobacco mosaic virus in explicit solution.