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Equilibrium sampling by reweighting nonequilibrium simulation trajectories
Yang, C; Wan, B; Xu, S; Wang, YT; Zhou, X; Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.
2016
发表期刊PHYSICAL REVIEW E
卷号93期号:3页码:33309
文章类型Article
摘要Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.
学科领域Physics
资助者NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences
DOIhttp://dx.doi.org/10.1103/PhysRevE.93.033309
关键词[WOS]MOLECULAR-DYNAMICS SIMULATIONS ; FREE-ENERGY DIFFERENCES ; MONTE-CARLO ; JARZYNSKIS EQUALITY ; TRANSITIONS ; GLASSES ; LIQUIDS ; ERROR ; FORCE
收录类别SCI
语种英语
资助者NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; NSFC [11175250] ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Open Project from the State Key Laboratory of Theoretical Physics ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences ; Hundred Talent Program of the Chinese Academy of Sciences
WOS类目Physics, Fluids & Plasmas ; Physics, Mathematical
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/21728
专题理论物理所SCI论文
通讯作者Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.
推荐引用方式
GB/T 7714
Yang, C,Wan, B,Xu, S,et al. Equilibrium sampling by reweighting nonequilibrium simulation trajectories[J]. PHYSICAL REVIEW E,2016,93(3):33309.
APA Yang, C,Wan, B,Xu, S,Wang, YT,Zhou, X,&Zhou, X .(2016).Equilibrium sampling by reweighting nonequilibrium simulation trajectories.PHYSICAL REVIEW E,93(3),33309.
MLA Yang, C,et al."Equilibrium sampling by reweighting nonequilibrium simulation trajectories".PHYSICAL REVIEW E 93.3(2016):33309.
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