Enhanced sampling in molecular dynamics
文献类型：期刊论文
| 作者 | Yang, Yi Isaac1; Shao, Qiang2 ; Zhang, Jun3; Yang, Lijiang4; Gao, Yi Qin1,4,5,6
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| 刊名 | JOURNAL OF CHEMICAL PHYSICS
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| 出版日期 | 2019-08-21 |
| 卷号 | 151期号:7页码:9 |
| ISSN号 | 0021-9606 |
| DOI | 10.1063/1.5109531 |
| 通讯作者 | Gao, Yi Qin(gaoyq@pku.edu.cn) |
| 英文摘要 | Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling. |
| WOS关键词 | COARSE-GRAINED MODELS ; FREE-ENERGY ; COMPUTER-SIMULATION ; LOCAL ELEVATION ; FOLDING PATHWAY ; RARE EVENTS ; WATER ; EFFICIENT ; OPTIMIZATION ; DEPENDENCE |
| 资助项目 | National Natural Science Foundation of China[21573006] ; National Natural Science Foundation of China[21821004] ; National Natural Science Foundation of China[21873007] ; National Key R&D Program of China[2017YFA0204702] |
| WOS研究方向 | Chemistry ; Physics |
| 语种 | 英语 |
| WOS记录号 | WOS:000482456100011 |
| 出版者 | AMER INST PHYSICS |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/288825]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Gao, Yi Qin |
| 作者单位 | 1.Shenzhen Bay Lab, Inst Syst Biol, Shenzhen 518055, Guangdong, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Mat Med, Key Lab Receptor Res, Drug Discovery & Design Ctr, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China 3.Free Univ Berlin, Dept Math & Comp Sci, Arnimallee 6, D-14195 Berlin, Germany 4.Peking Univ, Inst Theoret & Computat Chem, Coll Chem & Mol Engn, Beijing 100871, Peoples R China 5.Peking Univ, Biomed Pioneering Innovat Ctr, Beijing 100871, Peoples R China 6.Beijing Natl Lab Mol Sci, Beijing 100871, Peoples R China |
| 推荐引用方式 GB/T 7714 | Yang, Yi Isaac,Shao, Qiang,Zhang, Jun,et al. Enhanced sampling in molecular dynamics[J]. JOURNAL OF CHEMICAL PHYSICS,2019,151(7):9. |
| APA | Yang, Yi Isaac,Shao, Qiang,Zhang, Jun,Yang, Lijiang,&Gao, Yi Qin.(2019).Enhanced sampling in molecular dynamics.JOURNAL OF CHEMICAL PHYSICS,151(7),9. |
| MLA | Yang, Yi Isaac,et al."Enhanced sampling in molecular dynamics".JOURNAL OF CHEMICAL PHYSICS 151.7(2019):9. |
入库方式： OAI收割
来源：上海药物研究所
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