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Gong, LC; Zhou, X; Ouyang, ZC; Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
Reweighted ensemble dynamics simulations: Theory, improvement, and application
Source PublicationCHINESE PHYSICS B
Language英语
KeywordEnsemble Dynamics Simulations Peptides Enhanced Sampling Metastable States
AbstractBased on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.
2015
Volume24Issue:6Pages:60202
Subject AreaPhysics
DOIhttp://dx.doi.org/10.1088/1674-1056/24/6/060202
Indexed BySCI
Funding OrganizationHundred of Talents Program in the Chinese Academy of Sciences ; Hundred of Talents Program in the Chinese Academy of Sciences ; Hundred of Talents Program in the Chinese Academy of Sciences ; Hundred of Talents Program in the Chinese Academy of Sciences ; Max Planck Society ; Max Planck Society ; Max Planck Society ; Max Planck Society ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology
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Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/20979
Collection理论物理所科研产出_SCI论文
Corresponding AuthorZhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
Recommended Citation
GB/T 7714
Gong, LC,Zhou, X,Ouyang, ZC,et al. Reweighted ensemble dynamics simulations: Theory, improvement, and application[J]. CHINESE PHYSICS B,2015,24(6):60202.
APA Gong, LC,Zhou, X,Ouyang, ZC,&Zhou, X .(2015).Reweighted ensemble dynamics simulations: Theory, improvement, and application.CHINESE PHYSICS B,24(6),60202.
MLA Gong, LC,et al."Reweighted ensemble dynamics simulations: Theory, improvement, and application".CHINESE PHYSICS B 24.6(2015):60202.
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