Replica Exchange Molecular Dynamics
文献类型：期刊论文
| 作者 | Peng, Cheng1,2; Wu, Leyun1,2; Xu, Zhijian1,2 ; Zhu, Weiliang1,2
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| 刊名 | PROGRESS IN CHEMISTRY
 |
| 出版日期 | 2022-02-20 |
| 卷号 | 34期号:2页码:384-396 |
| 关键词 | replica exchange molecular dynamics variation sampling efficiency number of replica conformational change |
| ISSN号 | 1005-281X |
| DOI | 10.7536/PC201226 |
| 通讯作者 | Xu, Zhijian(zjxu@simm.ac.cn) ; Zhu, Weiliang(wlzhu@simm.ac.cn) |
| 英文摘要 | Replica exchange molecular dynamics (REMD) is a kind of enhanced sampling algorithm that has been widely used in the study of protein conformation changes with their free energy landscape. Due to its rigorous principle and high sampling efficiency, researches on the optimization and development of the conventional REMD method have also sprung up, and have been in the ascendant recently, which greatly enhances its sampling efficiency and expands its application. However, those REMD variations usually have specific application, making it difficult to choose suitable REMD variations in practical application. Therefore, it is of great significance to summarize the REMD variations for understanding their advantages and disadvantages and for choosing suitable REMD variations. Here, we review recent development of the REMD variations from the perspective of their principle, and classify them into six types of methods ; I) improving the approach and swapping rate of replica exchange, II) reducing the potential energy on exchange attempts to reduce the number of replica, III) Hamiltonians replica exchange molecular dynamics, IV) adjusting simulation process to improve sampling efficiency, V) changing the sampling methods, VI) adapting to heterogeneous and distributed computing environment. We hope that this review may be helpful in the understanding, application, and further improvement of the various REMD variations. |
| WOS关键词 | CONFORMATIONAL-CHANGE ; GLOBAL OPTIMIZATION ; BINDING-AFFINITY ; SIMULATIONS ; STATE ; CONVERGENCE ; EFFICIENCY ; MEMBRANE ; PEPTIDES ; SYSTEMS |
| 资助项目 | National Key Research and Development Program[2016YFA0502301] ; National Science & Technology Major ProjectKey New Drug Creation and Manufacturing Program. China[2018ZX09711002] |
| WOS研究方向 | Chemistry |
| 语种 | 英语 |
| WOS记录号 | WOS:000793177800003 |
| 出版者 | CHINESE ACAD SCIENCES |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/301001]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Xu, Zhijian; Zhu, Weiliang |
| 作者单位 | 1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China |
| 推荐引用方式 GB/T 7714 | Peng, Cheng,Wu, Leyun,Xu, Zhijian,et al. Replica Exchange Molecular Dynamics[J]. PROGRESS IN CHEMISTRY,2022,34(2):384-396. |
| APA | Peng, Cheng,Wu, Leyun,Xu, Zhijian,&Zhu, Weiliang.(2022).Replica Exchange Molecular Dynamics.PROGRESS IN CHEMISTRY,34(2),384-396. |
| MLA | Peng, Cheng,et al."Replica Exchange Molecular Dynamics".PROGRESS IN CHEMISTRY 34.2(2022):384-396. |
入库方式： OAI收割
来源：上海药物研究所
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