论文标题
全球自由能景观作为当地地图的平稳结合
Global free energy landscapes as a smoothly joined collection of local maps
论文作者
论文摘要
增强的采样技术已成为计算化学和物理学的重要工具,在该工具中,它们被应用于在传统模拟无法访问的时间尺度上发生的样本激活过程。尽管它们很受欢迎,但众所周知,它们的限制阻碍了他们对复杂问题的应用。核心问题在于需要使用少量的集体变量(CVS)来描述系统。所选CVS未正确描述的任何缓慢程度的自由度都会阻碍采样效率。但是,包括与描述所研究的激活过程无关的变量,对配置空间的探索也受到阻碍。本文介绍了用于加速采样的景观的自适应地形(ATLAS),这是一种能够与许多CV合作的新偏见方法。地图集的根概念是应用一个分裂策略,其中高维CVS空间分为盆地,每一个都由自动确定的,低维的变量集来描述。脾气暴躁的元动力偏差是这些局部变量的函数。指标功能与盆地关联的局部开关和关闭局部偏见,因此采样是在低维CV空间的集合上进行的,这些偏见平稳地组合以产生有效的高维偏置。无偏的玻尔兹曼分布通过重新恢复,使构象和热力学特性的评估直接评估。随着模拟发现新的(META)稳定状态,可以迭代地更新本地盆地中自由化景观的分解。
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite their popularity, it is well known that they have constraints that hinder their applications to complex problems. The core issue lies in the need to describe the system using a small number of collective variables (CVs). Any slow degree of freedom that is not properly described by the chosen CVs will hinder sampling efficiency. However, exploration of configuration space is also hampered by including variables that are not relevant to describe the activated process under study. This paper presents the Adaptive Topography of Landscape for Accelerated Sampling (ATLAS), a new biasing method capable of working with many CVs. The root idea of ATLAS is to apply a divide-and-conquer strategy where the high-dimensional CVs space is divided into basins, each of which is described by an automatically-determined, low-dimensional set of variables. A well-tempered metadynamics-like bias is constructed as a function of these local variables. Indicator functions associated with the basins switch on and off the local biases, so that the sampling is performed on a collection of low-dimensional CV spaces, that are smoothly combined to generate an effectively high-dimensional bias. The unbiased Boltzmann distribution is recovered through reweighing, making the evaluation of conformational and thermodynamic properties straightforward. The decomposition of the free-energy landscape in local basins can be updated iteratively as the simulation discovers new (meta)stable states.