论文标题
增强分子动力学模拟的采样方法
Enhanced sampling methods for molecular dynamics simulations
论文作者
论文摘要
增强的采样算法已作为扩展分子动力学仿真的实用性的强大方法,并允许在给定数量的模拟时间内对复杂系统的较大构型构型空间进行采样。这篇综述旨在介绍许多计算方法的统一原理和差异,用于增强生物分子,软物质和分子晶体的分子模拟中的采样。的确,尽管这种方法显然有丰富的和差异,但其核心原理可以归结为相对有限的统计和物理原理。为了启用比较,使用相似的术语和符号引入各种方法。然后,我们说明哪些不同方法从哪些不同的方法结合了较小的增强抽样概念的原理。这篇综述旨在理解分子动力学模拟和统计物理学的基础知识,他们希望更深入地了解这些思想是基于各种增强的采样方法及其之间的关系的思想。这项生活审查旨在更新,以继续反映出在文献中继续出现的抽样方法。
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.