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题名: Reweighted ensemble dynamics simulations: Theory, improvement, and application
作者: Gong, LC;  Zhou, X;  Ouyang, ZC
刊名: CHINESE PHYSICS B
出版日期: 2015
卷号: 24, 期号:6, 页码:60202
关键词: ensemble dynamics simulations ;  peptides ;  enhanced sampling ;  metastable states
学科分类: Physics
DOI: http://dx.doi.org/10.1088/1674-1056/24/6/060202
通讯作者: Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
文章类型: Article
英文摘要: 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.
类目[WOS]: Physics, Multidisciplinary
关键词[WOS]: FREE-ENERGY ;  MOLECULAR-DYNAMICS ;  INFREQUENT EVENTS ;  POTENTIAL-ENERGY ;  SYSTEMS ;  DISTRIBUTIONS ;  TRANSITIONS ;  LANDSCAPES ;  ALGORITHM ;  SURFACES
收录类别: SCI
项目资助者: Hundred of Talents Program in the Chinese Academy of Sciences ;  Max Planck Society ;  Korea Ministry of Education, Science and Technology
语种: 英语
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/20979
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Recommended Citation:
Gong, LC,Zhou, X,Ouyang, ZC. Reweighted ensemble dynamics simulations: Theory, improvement, and application[J]. CHINESE PHYSICS B,2015,24(6):60202.
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