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Reweighted ensemble dynamics simulations: Theory, improvement, and application
Gong, LC; Zhou, X; Ouyang, ZC; Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
2015
发表期刊CHINESE PHYSICS B
卷号24期号:6页码:60202
文章类型Article
摘要Based 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.
关键词Ensemble Dynamics Simulations Peptides Enhanced Sampling Metastable States
学科领域Physics
资助者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 ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology ; 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 ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology
DOIhttp://dx.doi.org/10.1088/1674-1056/24/6/060202
关键词[WOS]FREE-ENERGY ; MOLECULAR-DYNAMICS ; INFREQUENT EVENTS ; POTENTIAL-ENERGY ; SYSTEMS ; DISTRIBUTIONS ; TRANSITIONS ; LANDSCAPES ; ALGORITHM ; SURFACES
收录类别SCI
语种英语
资助者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 ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology ; 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 ; Korea Ministry of Education, Science and Technology ; Korea Ministry of Education, Science and Technology
WOS类目Physics, Multidisciplinary
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/20979
专题理论物理所2015年知识产出
通讯作者Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
推荐引用方式
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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