基于结构约束的层次深势模型的高效粗粒度建模。

IF 5.3 2区 化学 Q1 CHEMISTRY, MEDICINAL
Qi Huang, Yedi Li, Lei Zhu, Wenjie Yu
{"title":"基于结构约束的层次深势模型的高效粗粒度建模。","authors":"Qi Huang, Yedi Li, Lei Zhu, Wenjie Yu","doi":"10.1021/acs.jcim.4c02042","DOIUrl":null,"url":null,"abstract":"<p><p>Coarse-grained molecular dynamics is a powerful approach for simulating large-scale systems by reducing the number of degrees of freedom. Nonetheless, the development of accurate coarse-grained force fields remains challenging, particularly for complex systems, such as polymers. In this study, we introduce a novel framework, hierarchical deep potential with structure constraints (HDP-SC), designed to construct coarse-grained force fields for polymer materials. Our methodology integrates a prior energy term obtained through direct Boltzmann inversion with a deep neural network potential, which is trained using hierarchical bead environment descriptors. This framework facilitates the reproduction of structural distributions and the potential of mean force, thus enhancing the accuracy and efficiency of the coarse-grained model. We validate our approach using polystyrene systems, demonstrating that the HDP-SC model not only successfully reproduces the structural properties of these systems but also remains applicable at larger scales. Our findings underscore the promise of machine learning-based techniques in advancing the development of coarse-grained force fields for polymer materials.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"3203-3214"},"PeriodicalIF":5.3000,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Hierarchical Deep Potential with Structure Constraints for Efficient Coarse-Grained Modeling.\",\"authors\":\"Qi Huang, Yedi Li, Lei Zhu, Wenjie Yu\",\"doi\":\"10.1021/acs.jcim.4c02042\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Coarse-grained molecular dynamics is a powerful approach for simulating large-scale systems by reducing the number of degrees of freedom. Nonetheless, the development of accurate coarse-grained force fields remains challenging, particularly for complex systems, such as polymers. In this study, we introduce a novel framework, hierarchical deep potential with structure constraints (HDP-SC), designed to construct coarse-grained force fields for polymer materials. Our methodology integrates a prior energy term obtained through direct Boltzmann inversion with a deep neural network potential, which is trained using hierarchical bead environment descriptors. This framework facilitates the reproduction of structural distributions and the potential of mean force, thus enhancing the accuracy and efficiency of the coarse-grained model. We validate our approach using polystyrene systems, demonstrating that the HDP-SC model not only successfully reproduces the structural properties of these systems but also remains applicable at larger scales. Our findings underscore the promise of machine learning-based techniques in advancing the development of coarse-grained force fields for polymer materials.</p>\",\"PeriodicalId\":44,\"journal\":{\"name\":\"Journal of Chemical Information and Modeling \",\"volume\":\" \",\"pages\":\"3203-3214\"},\"PeriodicalIF\":5.3000,\"publicationDate\":\"2025-04-14\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Information and Modeling \",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jcim.4c02042\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/3/22 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MEDICINAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c02042","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/3/22 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0

摘要

粗粒度分子动力学是通过减少自由度来模拟大规模系统的有力方法。然而,精确的粗粒度力场的发展仍然具有挑战性,特别是对于复杂的系统,如聚合物。在这项研究中,我们引入了一个新的框架,层次结构约束深层电位(HDP-SC),旨在构建聚合物材料的粗粒度力场。我们的方法将通过直接玻尔兹曼反演获得的先验能量项与使用分层头环境描述符训练的深度神经网络势相结合。该框架有利于再现结构分布和平均力的潜力,从而提高了粗粒度模型的准确性和效率。我们用聚苯乙烯系统验证了我们的方法,证明HDP-SC模型不仅成功地再现了这些系统的结构特性,而且在更大的尺度上仍然适用。我们的发现强调了基于机器学习的技术在推进聚合物材料粗粒度力场发展方面的前景。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Hierarchical Deep Potential with Structure Constraints for Efficient Coarse-Grained Modeling.

Coarse-grained molecular dynamics is a powerful approach for simulating large-scale systems by reducing the number of degrees of freedom. Nonetheless, the development of accurate coarse-grained force fields remains challenging, particularly for complex systems, such as polymers. In this study, we introduce a novel framework, hierarchical deep potential with structure constraints (HDP-SC), designed to construct coarse-grained force fields for polymer materials. Our methodology integrates a prior energy term obtained through direct Boltzmann inversion with a deep neural network potential, which is trained using hierarchical bead environment descriptors. This framework facilitates the reproduction of structural distributions and the potential of mean force, thus enhancing the accuracy and efficiency of the coarse-grained model. We validate our approach using polystyrene systems, demonstrating that the HDP-SC model not only successfully reproduces the structural properties of these systems but also remains applicable at larger scales. Our findings underscore the promise of machine learning-based techniques in advancing the development of coarse-grained force fields for polymer materials.

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
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
×
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