OPES-eABF混合采样方法中快速勘探与精确加权的结合。

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Andreas Hulm,Robert P Schiller,Christian Ochsenfeld
{"title":"OPES-eABF混合采样方法中快速勘探与精确加权的结合。","authors":"Andreas Hulm,Robert P Schiller,Christian Ochsenfeld","doi":"10.1021/acs.jctc.5c00395","DOIUrl":null,"url":null,"abstract":"On-the-fly probability enhanced sampling (OPES) has recently been introduced [Invernizzi, M.; Parrinello, M. J. Chem. Theory Comput. 2022, 18, 3988-3996], with important improvements over the highly popular metadynamics methods. In our work, we introduce a new combination of OPES with the extended-system adaptive biasing force (eABF) method. We show that the resulting OPES-eABF hybrid is highly robust to the choice of input parameters, while ensuring faster exploration of configuration space than the original OPES. The only critical parameter of OPES-eABF is the coupling width to the extended-system, for which we introduce an automatic algorithm based on a short initial unbiased simulation, such that OPES-eABF requires minimal user intervention. Additionally, we show that due to the decoupling of the physical system from the time-dependent potential, unbiased probabilities of visited configurations are recovered highly accurately.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"13 1","pages":""},"PeriodicalIF":5.7000,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.\",\"authors\":\"Andreas Hulm,Robert P Schiller,Christian Ochsenfeld\",\"doi\":\"10.1021/acs.jctc.5c00395\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"On-the-fly probability enhanced sampling (OPES) has recently been introduced [Invernizzi, M.; Parrinello, M. J. Chem. Theory Comput. 2022, 18, 3988-3996], with important improvements over the highly popular metadynamics methods. In our work, we introduce a new combination of OPES with the extended-system adaptive biasing force (eABF) method. We show that the resulting OPES-eABF hybrid is highly robust to the choice of input parameters, while ensuring faster exploration of configuration space than the original OPES. The only critical parameter of OPES-eABF is the coupling width to the extended-system, for which we introduce an automatic algorithm based on a short initial unbiased simulation, such that OPES-eABF requires minimal user intervention. Additionally, we show that due to the decoupling of the physical system from the time-dependent potential, unbiased probabilities of visited configurations are recovered highly accurately.\",\"PeriodicalId\":45,\"journal\":{\"name\":\"Journal of Chemical Theory and Computation\",\"volume\":\"13 1\",\"pages\":\"\"},\"PeriodicalIF\":5.7000,\"publicationDate\":\"2025-06-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Theory and Computation\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jctc.5c00395\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Theory and Computation","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jctc.5c00395","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0

摘要

动态概率增强抽样(OPES)最近被引入[Invernizzi, M.;Parrinello, m.j. Chem。理论计算,2022,18,3988-3996],对非常流行的元动力学方法进行了重要改进。在我们的工作中,我们引入了一种新的OPES与扩展系统自适应偏置力(eABF)方法的组合。结果表明,所得到的OPES- eabf混合算法对输入参数的选择具有高度鲁棒性,同时确保比原始OPES更快地探索配置空间。OPES-eABF的唯一关键参数是与扩展系统的耦合宽度,为此我们引入了一种基于短初始无偏模拟的自动算法,使得OPES-eABF需要最少的用户干预。此外,我们表明,由于物理系统与时间相关势的解耦,访问组态的无偏概率被高度准确地恢复。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.
On-the-fly probability enhanced sampling (OPES) has recently been introduced [Invernizzi, M.; Parrinello, M. J. Chem. Theory Comput. 2022, 18, 3988-3996], with important improvements over the highly popular metadynamics methods. In our work, we introduce a new combination of OPES with the extended-system adaptive biasing force (eABF) method. We show that the resulting OPES-eABF hybrid is highly robust to the choice of input parameters, while ensuring faster exploration of configuration space than the original OPES. The only critical parameter of OPES-eABF is the coupling width to the extended-system, for which we introduce an automatic algorithm based on a short initial unbiased simulation, such that OPES-eABF requires minimal user intervention. Additionally, we show that due to the decoupling of the physical system from the time-dependent potential, unbiased probabilities of visited configurations are recovered highly accurately.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信