Enhanced sampling in molecular dynamics simulations and their latest applications-A review

被引:17
作者
Shen, Wenhui [1 ,2 ]
Zhou, Tong [1 ,2 ]
Shi, Xinghua [1 ,2 ]
机构
[1] Natl Ctr Nanosci & Technol, Lab Theoret & Computat Nanosci, Beijing 100190, Peoples R China
[2] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
基金
国家重点研发计划; 中国国家自然科学基金;
关键词
molecular dynamics; enhanced sampling; free energy barrier; time scale; biological system; FREE-ENERGY LANDSCAPE; HIGH-TEMPERATURE EQUATION; HISTOGRAM ANALYSIS METHOD; PROTEIN-FOLDING KINETICS; REPLICA-EXCHANGE; MONTE-CARLO; WEIGHTED-ENSEMBLE; BINDING PATHWAYS; MULTICANONICAL ENSEMBLE; CONFORMATIONAL-CHANGE;
D O I
10.1007/s12274-023-6311-9
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Molecular dynamics (MD) simulations are capable of reproducing dynamic evolution at the molecular scale, but are limited by temporal scales. Enhanced sampling has emerged as a powerful tool to improve sampling efficiency, thereby extending the simulation timescales of a range of simulation studies in materials, chemistry, biology, nanoscience, and related fields. Here, we provide a systematic overview of established enhanced sampling methods and clarify the principles and interconnections between these methods. Furthermore, we categorically elaborate on the state-of-the-art applications of enhanced sampling in the last five years. Through these exemplified applications, we discuss the unique advantages of this technique, showing the prospects and challenges for its future development. This review could help researchers in different fields gain a comprehensive understanding of the enhanced sampling technique, and jointly facilitate its application and advancement.
引用
收藏
页码:13474 / 13497
页数:24
相关论文
共 285 条
[1]  
Berg BA, 1999, Arxiv, DOI arXiv:cond-mat/9909236
[2]   Ensuring mixing efficiency of replica-exchange molecular dynamics simulations [J].
Abraham, Mark J. ;
Gready, Jill E. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (07) :1119-1128
[3]   Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration [J].
Abrams, Cameron ;
Bussi, Giovanni .
ENTROPY, 2014, 16 (01) :163-199
[4]   Computational Estimation of Microsecond to Second Atomistic Folding Times [J].
Adhikari, Upendra ;
Mostofian, Barmak ;
Copperman, Jeremy ;
Subramanian, Sundar Raman ;
Petersen, Andrew A. ;
Zuckerman, Daniel M. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2019, 141 (16) :6519-6526
[5]   Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling [J].
Ahn, Surl-Hee ;
Ojha, Anupam A. ;
Amaro, Rommie E. ;
McCammon, J. Andrew .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2021, 17 (12) :7938-7951
[6]  
[Anonymous], 1951, Mathematics of Statistics
[7]   Weighted ensemble: Recent mathematical developments [J].
Aristoff, D. ;
Copperman, J. ;
Simpson, G. ;
Webber, R. J. ;
Zuckerman, D. M. .
JOURNAL OF CHEMICAL PHYSICS, 2023, 158 (01)
[8]   An ergodic theorem for the weighted ensemble method [J].
Aristoff, David .
JOURNAL OF APPLIED PROBABILITY, 2022, 59 (01) :152-166
[9]  
Aristoff D, 2020, MULTISCALE MODEL SIM, V18, P646, DOI [10.1137/18M1212100, 10.1137/18m1212100]
[10]   ANALYSIS AND OPTIMIZATION OF WEIGHTED ENSEMBLE SAMPLING [J].
Aristoff, David .
ESAIM-MATHEMATICAL MODELLING AND NUMERICAL ANALYSIS-MODELISATION MATHEMATIQUE ET ANALYSE NUMERIQUE, 2018, 52 (04) :1219-1238