High-Efficiency Microiterative Optimization in QM/MM Simulations of Large Flexible Systems

doi:10.1021/acs.jctc.6b00547

	High-Efficiency Microiterative Optimization in QM/MM Simulations of Large Flexible Systems
	He, Xiaohu; Xie, Peng; Han, Keli; Zhang, Yan
刊名	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
	2016-09-01
卷号	12 期号:9 页码:4632-4643
ISSN号	1549-9618
DOI	10.1021/acs.jctc.6b00547
文献子类	Article
英文摘要	We present here a double-optimizations-of-buffer-region (DOBR) microiterative scheme for high-efficiency energy minimizations of large, flexible systems in combined quantum-mechanical/molecular-mechanical (QM/MM) calculations. In the DOBR scheme, an entire system is divided into three regions: the core, buffer, and outer regions. The core region includes QM atoms and the MM atoms within a cutoff distance R-1 to the QM atoms (denoted by MM1 atoms), and the buffer region consists of MM atoms within another cutoff distance R-2 to MM1 atoms. Each DOBR microcycle involves two steps: First, QM atoms are assigned electrostatic potential (ESP) charges, and the buffer and outer regions are optimized at the MM level with the core region kept frozen. Second, the core and buffer regions are optimized at the QM/MM level using the electrostatic embedding with the outer region kept frozen. The two steps are repeated until two optimizations converge at one structure. The DOBR scheme was tested in the optimizations of nucleobases solvated in water spheres of 30 angstrom radius, where the initial geometries were extracted from the trajectories of classical molecular dynamics simulations, and the cutoff distances. R-1 and R-2 were set to 5.0 and 4.0 angstrom, respectively. For, comparisons, the optimizations were also carried out by a "standard" scheme without microiteration and by the two-region microiterative (TRM) method. We found that the averaged number of QM calculations for the DOBR scheme is only similar to 1% of that of the standard scheme and similar to 6% of the TRM approach. The promising results indicate that the DOBR scheme could significantly increase the efficiency of geometry optimizations for large, flexible systems in QM/MM calculations.
WOS关键词	MOLECULAR-ORBITAL METHODS ; POTENTIAL-ENERGY SURFACE ; TRANSITION-STATE SEARCH ; GAUSSIAN-TYPE BASIS ; GEOMETRY OPTIMIZATION ; BASIS-SETS ; MECHANICAL CALCULATIONS ; REDISTRIBUTED CHARGE ; ENZYMATIC-REACTIONS ; BIOLOGICAL-SYSTEMS
WOS研究方向	Chemistry ; Physics
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000383315700041
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/169988]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者	Han, Keli; Zhang, Yan
作者单位	Chinese Acad Sci, State Key Lab Mol React Dynam, Dalian Inst Chem Phys, Zhongshan Rd 457, Dalian 116023, Peoples R China
推荐引用方式 GB/T 7714	He, Xiaohu,Xie, Peng,Han, Keli,et al. High-Efficiency Microiterative Optimization in QM/MM Simulations of Large Flexible Systems[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2016,12(9):4632-4643.
APA	He, Xiaohu,Xie, Peng,Han, Keli,&Zhang, Yan.(2016).High-Efficiency Microiterative Optimization in QM/MM Simulations of Large Flexible Systems.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,12(9),4632-4643.
MLA	He, Xiaohu,et al."High-Efficiency Microiterative Optimization in QM/MM Simulations of Large Flexible Systems".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12.9(2016):4632-4643.