Combine umbrella sampling with integrated tempering method for efficient   and accurate calculation of free energy changes of complex energy   surface

doi:10.1063/1.4887340

CORC > 北京大学 > 化学与分子工程学院

	Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface
	Yang, Mingjun ; Yang, Lijiang ; Gao, Yiqin ; Hu, Hao
刊名	journal of chemical physics
	2014
关键词	MOLECULAR-DYNAMICS SIMULATIONS HISTOGRAM ANALYSIS METHOD MONTE-CARLO MULTICANONICAL ENSEMBLE LIKELIHOOD APPROACH PHASE-TRANSITIONS SLOW-GROWTH DISTRIBUTIONS THERMODYNAMICS BIOMOLECULES
DOI	10.1063/1.4887340
英文摘要	Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes. (C) 2014 AIP Publishing LLC.; Physics, Atomic, Molecular & Chemical; SCI(E); EI; PubMed; 2; ARTICLE; haohu@hku.hk; 4; 044108; 141
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/188843]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Yang, Mingjun,Yang, Lijiang,Gao, Yiqin,et al. Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface[J]. journal of chemical physics,2014.
APA	Yang, Mingjun,Yang, Lijiang,Gao, Yiqin,&Hu, Hao.(2014).Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface.journal of chemical physics.
MLA	Yang, Mingjun,et al."Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface".journal of chemical physics (2014).