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	Effectively explore metastable states of proteins by adaptive nonequilibrium driving simulations
	Wan, Biao1; Xu, Shun1,2; Zhou, Xin1
刊名	Physical review e
	2017-03-09
卷号	95期号:3页码:10
ISSN号	2470-0045
DOI	10.1103/physreve.95.033304
通讯作者	Zhou, xin(xzhou@ucas.ac.cn)
英文摘要	Nonequilibrium drivings applied in molecular dynamics (md) simulations can efficiently extend the visiting range of protein conformations, but might compel systems to go far away from equilibrium and thus mainly explore irrelevant conformations. here we propose a general method, called adaptive nonequilibrium simulation (anes), to automatically adjust the external driving on the fly, based on the feedback of the short-time average response of system. thus, the anes approximately keeps the local equilibrium but efficiently accelerates the global motion. we illustrate the capability of the anes in highly efficiently exploring metastable conformations in the deca-alanine peptide and find that the 0.2-mu s anes approximately captures the important states and folding and unfolding pathways in the hp35 solution by comparing with the result of the recent 398-mu s equilibrium md simulation on anton
WOS关键词	MOLECULAR-DYNAMICS SIMULATIONS ; FREE-ENERGY LANDSCAPE ; FOLDING SIMULATIONS ; VILLIN HEADPIECE ; STRUCTURAL DYNAMICS ; AVERAGE FORCE ; SPECTROSCOPY ; ALGORITHM ; SUBDOMAIN ; EFFICIENT
WOS研究方向	Physics
WOS类目	Physics, Fluids & Plasmas ; Physics, Mathematical
语种	英语
出版者	AMER PHYSICAL SOC
WOS记录号	WOS:000396040800012
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2374224
专题	计算机网络信息中心
通讯作者	Zhou, Xin
作者单位	1.Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Supercomp Ctr, Comp Network Informat Ctr, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Wan, Biao,Xu, Shun,Zhou, Xin. Effectively explore metastable states of proteins by adaptive nonequilibrium driving simulations[J]. Physical review e,2017,95(3):10.
APA	Wan, Biao,Xu, Shun,&Zhou, Xin.(2017).Effectively explore metastable states of proteins by adaptive nonequilibrium driving simulations.Physical review e,95(3),10.
MLA	Wan, Biao,et al."Effectively explore metastable states of proteins by adaptive nonequilibrium driving simulations".Physical review e 95.3(2017):10.

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