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化学进展 2022, Vol. 34 Issue (2): 384-396 DOI: 10.7536/PC201226 前一篇   后一篇

• 综述 •

副本交换分子动力学

彭诚1,2, 吴乐云1,2, 徐志建1,2,*(), 朱维良1,2,*()   

  1. 1 中国科学院上海药物研究所药物发现与设计中心 上海 201203
    2 中国科学院大学 北京 100049
  • 收稿日期:2020-12-15 修回日期:2021-02-16 出版日期:2022-02-20 发布日期:2021-03-04
  • 通讯作者: 徐志建, 朱维良
  • 基金资助:
    国家重点研发计划项目(2016YFA0502301); 国家重大新药创制科技重大专项(2018ZX09711002)
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Replica Exchange Molecular Dynamics

Cheng Peng1,2, Leyun Wu1,2, Zhijian Xu1,2(), Weiliang Zhu1,2()   

  1. 1 Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences,Shanghai 201203, China
    2 University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2020-12-15 Revised:2021-02-16 Online:2022-02-20 Published:2021-03-04
  • Contact: Zhijian Xu, Weiliang Zhu
  • Supported by:
    National Key Research and Development Program(2016YFA0502301); National Science & Technology Major Project“Key New Drug Creation and Manufacturing Program”, China(2018ZX09711002)

副本交换分子动力学(REMD)是一种广泛应用于蛋白质功能性构象变化模拟及相应自由能计算的增强型采样算法。由于REMD理论严格且采样效率高,近年来备受关注,尤其是针对传统REMD方法的发展和优化,显著提高了REMD的采样效率,拓展了其应用范围。但是各种REMD新型方法的最佳适用范围也存在较大区别,使得如何选用合适的REMD方法成为实际应用的难题和挑战。因此,有必要对各种REMD方法及其应用进行阐述,深入比较各方法的优缺点及其实际应用体系。本综述从REMD的原理出发,回顾了近年来各类REMD方法的变形策略,以助于对REMD方法的理解、应用和继续改进。

关键词： 副本交换分子动力学, 变形, 采样效率, 副本数目, 构象变化

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.

Contents

1 Introduction

2 Temperature replica exchange molecular dynamics

3 Improve the approach and swapping rate of replica exchange

4 Reduce the potential energy on exchange attempts to reduce the number of replica

4.1 Deal with the explicit solvent

4.2 Reduce the freedom of solute

5 Hamiltonians replica exchange molecular dynamics

5.1 Adjust the formula of potential energy

5.2 Adopted into other enhanced sampling algorithms

5.3 Multidimensional replica exchange molecular dynamics

5.4 Introducing physical parameters in simulations

6 Adjust simulation process to improve sampling efficiency

6.1 The way of temperature control

6.2 The parameters in parallel replicas

6.3 Multilayer simulation in parallel replicas

6.4 Adjust initial structures

7 Sampling methods

8 Heterogeneous and distributed computing environment

9 Conclusion and outlook

Key words: replica exchange molecular dynamics, variation, sampling efficiency, number of replica, conformational change
()
表1 多维REMD方法列表。
Table 1 The list of multidimensional REMD.
Methods CVs* System ref
RSE-MTD dihedral angles, atomic distance, T organic, peptide 73⇓⇓~76
w-REXAMD dihedral boost parameters organic, peptide 80⇓~82
REUS/REST Distance, potential energy(T) protein-ligand 84
H-REMD/T-REMD Restraint strength, T RNA 85
ABMD+
REMD		 Rg, T organic 86
FEP/REST λ,T Protein-ligand 89⇓~91
Tq-REM q, T peptide, protein 92
ossPTMetaD NMA,T protein-ligand, protein 79
Multidimensional REMD pH, Ev, T peptide 93
图1 代表性REMD变形方法图解。T1-T4代表4个平行模拟副本,不同颜色表示不同模拟温度,其中Modified REMD方法中灰色表示冻结副本。在TIGER方法中,副本模拟有3个循环过程。
Fig. 1 The diagrams of representative REMD variations. T1-T4 refer to four parallel replicas, and different temperatures were colored specifically. The frozen replicas in the Modified REMD method were colored in gray. The TIGER simulation has three simulation cycles.
表2 REMD优化方法总结
Table 2 The summary of methods to improve the sampling efficiency of REMD
Methods to improve the sampling efficiency of REMD Examples
1.Improve the approach and swapping rate of replica exchange RPM, RSPM, Calvo’s all-pairs exchange, REMD-MSSA,infinite swapping REMD, DEWREM
2.Reduce the potential energy on exchange attempts 1)Deal with the explicit solvent hybrid REMD, kernel REMD, REMshH, vsREMD, hREMD
2)Reduce the freedom of solute PREMD, LREMD
3.Hamiltonians replica exchange molecular dynamics 1)Adjust the formula of potential energy H-REMD, vWREM, CREM, REX-TAMD, Q-REMD, REST1, REST2, REFT, gREST, FREM, MFREM, ResEx
2)Adopted into other enhanced sampling algorithms BE-MTD, essential dynamics, rex-GaMD, AMD, GaREUS, EDS, BP-REXMSλD
3)Multidimensional replica exchange molecular dynamics RSE-MTD, w-REXAMD, REUS/REST, 2D REMD, ossPTMetaD, FEP/REST, ABMD-REMD, Tq-REM, Multidimensional REMD
4)Introducing physical parameters in simulations V-REMD, surface-tension REMD, MSREMD, VTREMD
4.Adjust simulation
process		 1)Change the way of temperature control TIGER1, TIGER2, TIGER2h, TIGER2A, TIGER2hs, TIGER3, EE-REMD, CM-REMD, STMD, Modified REMD 1, Modified REMD 2
2)Adjust parameters in parallel replicas Reservoir REMD, REDS, Convective REMD
3)Multilayer simulation in parallel replicas MuSTAR MD, Multiplexed REMD, mQ-REMD
4)Adjust initial structures NUMD+REMD, Onsager-Machlup/REMD
5.Change the sampling methods Tsallis-REMD, RXSGLD, QM/MM-REMD, BOMD, SE-BOREMD, CPMD, ICMD, MCMD
6.Heterogeneous and distributed computing environment gREMD, HaRE, ASyncRE
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摘要

副本交换分子动力学