采样(信号处理)
计算机科学
术语
分子动力学
分歧(语言学)
符号
统计物理学
数据科学
管理科学
理论计算机科学
数学
物理
计算化学
化学
工程类
滤波器(信号处理)
算术
哲学
语言学
计算机视觉
作者
Hénin, Jérôme,Lelièvre, Tony,Shirts, Michael R.,Valsson, Omar,Delemotte, Lucie
出处
期刊:Cornell University - arXiv
日期:2022-03-03
被引量:5
标识
DOI:10.48550/arxiv.2202.04164
摘要
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation time. This review aims to present the unifying principles and differences of many of the computational methods currenly used for enhanced sampling in molecular simulations of biomolecules, soft matter and molecular crystals. Indeed, despite the apparent abundance and divergence of such methods, the principles at their core can be boiled down to a relatively limited number of statistical and physical principles. To enable comparisons, the various methods are introduced using similar terminology and notation. We then illustrate in which ways many different methods combine principles from a smaller class of enhanced sampling concepts. This review is intended for scientists with an understanding of the basics of molecular dynamics simulations and statistical physics who want a deeper understanding of the ideas that underlie various enhanced sampling methods and the relationships between them. This living review is intended to be updated to continue to reflect the wealth of sampling methods as they continue to emerge in the literature.
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