{"title":"Unified Approach to Enhanced Sampling","authors":"Michele Invernizzi, P. Piaggi, M. Parrinello","doi":"10.1103/physrevx.10.041034","DOIUrl":null,"url":null,"abstract":"The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods are often grouped into two broad families. On the one hand methods such as umbrella sampling and metadynamics that build a bias potential based on few order parameters or collective variables. On the other hand, tempering methods such as replica exchange that combine different thermodynamic ensembles in one single expanded ensemble. We instead adopt a unifying perspective, focusing on the target probability distribution sampled by the different methods. This allows us to introduce a new class of collective-variables-based bias potentials that can be used to sample any of the expanded ensembles normally sampled via replica exchange. We also provide a practical implementation, by properly adapting the iterative scheme of the recently developed on-the-fly probability enhanced sampling method [Invernizzi and Parrinello, J. Phys. Chem. Lett. 11.7 (2020)], which was originally introduced for metadynamics-like sampling. The resulting method is very general and can be used to achieve different types of enhanced sampling. It is also reliable and simple to use, since it presents only few and robust external parameters and has a straightforward reweighting scheme. Furthermore, it can be used with any number of parallel replicas. We show the versatility of our approach with applications to multicanonical and multithermal-multibaric simulations, thermodynamic integration, umbrella sampling, and combinations thereof.","PeriodicalId":8424,"journal":{"name":"arXiv: Computational Physics","volume":"4 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2020-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"41","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv: Computational Physics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1103/physrevx.10.041034","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 41
Abstract
The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods are often grouped into two broad families. On the one hand methods such as umbrella sampling and metadynamics that build a bias potential based on few order parameters or collective variables. On the other hand, tempering methods such as replica exchange that combine different thermodynamic ensembles in one single expanded ensemble. We instead adopt a unifying perspective, focusing on the target probability distribution sampled by the different methods. This allows us to introduce a new class of collective-variables-based bias potentials that can be used to sample any of the expanded ensembles normally sampled via replica exchange. We also provide a practical implementation, by properly adapting the iterative scheme of the recently developed on-the-fly probability enhanced sampling method [Invernizzi and Parrinello, J. Phys. Chem. Lett. 11.7 (2020)], which was originally introduced for metadynamics-like sampling. The resulting method is very general and can be used to achieve different types of enhanced sampling. It is also reliable and simple to use, since it presents only few and robust external parameters and has a straightforward reweighting scheme. Furthermore, it can be used with any number of parallel replicas. We show the versatility of our approach with applications to multicanonical and multithermal-multibaric simulations, thermodynamic integration, umbrella sampling, and combinations thereof.
采样问题是原子模拟的核心,多年来,人们提出了许多不同的增强采样方法来解决这个问题。这些方法通常分为两大类。一方面,伞式采样和元动力学等方法基于少量序参数或集体变量建立了偏置势。另一方面,回火方法,如副本交换,将不同的热力学集成在一个单一的扩展集成中。相反,我们采用统一的观点,关注不同方法抽样的目标概率分布。这使我们能够引入一类新的基于集体变量的偏置势,可用于对通常通过副本交换采样的任何扩展集合进行采样。我们还提供了一个实际的实现,通过适当地采用最近开发的动态概率增强采样方法的迭代方案[Invernizzi和Parrinello, J. Phys]。化学。Lett. 11.7(2020)],最初是为类似元动力学的采样而引入的。所得到的方法是非常通用的,可用于实现不同类型的增强采样。它还可靠且使用简单,因为它只提供少量且健壮的外部参数,并且具有直接的重加权方案。此外,它可以用于任意数量的并行副本。我们展示了我们的方法的多功能性,应用于多声道和多热-多压模拟,热力学集成,伞式采样及其组合。