Reweighted ensemble dynamics simulations: Theory, improvement, and application
文献类型：期刊论文
| 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 |
| 通讯作者 | Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China. |
| 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. |
| 学科主题 | Physics |
| 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 |
| 语种 | 英语 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/20979]  |
| 专题 | 理论物理研究所_理论物理所1978-2010年知识产出 |
| 推荐引用方式 GB/T 7714 | Gong, LC,Zhou, X,Ouyang, ZC. Reweighted ensemble dynamics simulations: Theory, improvement, and application[J]. CHINESE PHYSICS B,2015,24(6):60202. |
| APA | Gong, LC,Zhou, X,&Ouyang, ZC.(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. |
入库方式： OAI收割
来源：理论物理研究所
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