基于机器学习柔性电荷势的影子分子动力学。

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2025-04-08 Epub Date: 2025-03-14 DOI:10.1021/acs.jctc.5c00062
Cheng-Han Li, Mehmet Cagri Kaymak, Maksim Kulichenko, Nicholas Lubbers, Benjamin T Nebgen, Sergei Tretiak, Joshua Finkelstein, Daniel P Tabor, Anders M N Niklasson
{"title":"基于机器学习柔性电荷势的影子分子动力学。","authors":"Cheng-Han Li, Mehmet Cagri Kaymak, Maksim Kulichenko, Nicholas Lubbers, Benjamin T Nebgen, Sergei Tretiak, Joshua Finkelstein, Daniel P Tabor, Anders M N Niklasson","doi":"10.1021/acs.jctc.5c00062","DOIUrl":null,"url":null,"abstract":"<p><p>We present an extended Lagrangian shadow molecular dynamics scheme with an interatomic Born-Oppenheimer potential determined by the relaxed atomic charges of a second-order charge equilibration model. To parametrize the charge equilibration model, we use machine learning with neural networks to determine the environment-dependent electronegativities and chemical hardness parameters for each atom, in addition to the charge-independent energy and force terms. The approximate shadow molecular dynamics potential in combination with the extended Lagrangian formulation improves the numerical stability and reduces the number of Coulomb potential calculations required to evaluate accurate conservative forces. We demonstrate efficient and accurate simulations with excellent long-term stability of the molecular dynamics trajectories. The significance of choosing fixed or environment-dependent electronegativities and chemical hardness parameters is evaluated. Finally, we compute the infrared spectrum of molecules via the dipole autocorrelation function and compare to experiments to highlight the accuracy of the shadow molecular dynamics scheme with a machine learned flexible charge potential.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"3658-3675"},"PeriodicalIF":5.7000,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Shadow Molecular Dynamics with a Machine Learned Flexible Charge Potential.\",\"authors\":\"Cheng-Han Li, Mehmet Cagri Kaymak, Maksim Kulichenko, Nicholas Lubbers, Benjamin T Nebgen, Sergei Tretiak, Joshua Finkelstein, Daniel P Tabor, Anders M N Niklasson\",\"doi\":\"10.1021/acs.jctc.5c00062\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>We present an extended Lagrangian shadow molecular dynamics scheme with an interatomic Born-Oppenheimer potential determined by the relaxed atomic charges of a second-order charge equilibration model. To parametrize the charge equilibration model, we use machine learning with neural networks to determine the environment-dependent electronegativities and chemical hardness parameters for each atom, in addition to the charge-independent energy and force terms. The approximate shadow molecular dynamics potential in combination with the extended Lagrangian formulation improves the numerical stability and reduces the number of Coulomb potential calculations required to evaluate accurate conservative forces. We demonstrate efficient and accurate simulations with excellent long-term stability of the molecular dynamics trajectories. The significance of choosing fixed or environment-dependent electronegativities and chemical hardness parameters is evaluated. Finally, we compute the infrared spectrum of molecules via the dipole autocorrelation function and compare to experiments to highlight the accuracy of the shadow molecular dynamics scheme with a machine learned flexible charge potential.</p>\",\"PeriodicalId\":45,\"journal\":{\"name\":\"Journal of Chemical Theory and Computation\",\"volume\":\" \",\"pages\":\"3658-3675\"},\"PeriodicalIF\":5.7000,\"publicationDate\":\"2025-04-08\",\"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.5c00062\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/3/14 0:00:00\",\"PubModel\":\"Epub\",\"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.5c00062","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/3/14 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0

摘要

我们提出了一个扩展的拉格朗日阴影分子动力学格式,该格式具有原子间Born-Oppenheimer势,该势由二阶电荷平衡模型中的松弛原子电荷决定。为了参数化电荷平衡模型,我们使用机器学习和神经网络来确定每个原子与环境相关的电负性和化学硬度参数,以及与电荷无关的能量和力项。近似阴影分子动力学势与扩展拉格朗日公式相结合,提高了数值稳定性,减少了计算精确保守力所需的库仑势的次数。我们展示了高效和准确的分子动力学轨迹模拟,具有良好的长期稳定性。评价了选择固定或环境相关电负性参数和化学硬度参数的意义。最后,我们通过偶极自相关函数计算分子的红外光谱,并与实验进行比较,以突出机器学习柔性电荷势的阴影分子动力学方案的准确性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Shadow Molecular Dynamics with a Machine Learned Flexible Charge Potential.

We present an extended Lagrangian shadow molecular dynamics scheme with an interatomic Born-Oppenheimer potential determined by the relaxed atomic charges of a second-order charge equilibration model. To parametrize the charge equilibration model, we use machine learning with neural networks to determine the environment-dependent electronegativities and chemical hardness parameters for each atom, in addition to the charge-independent energy and force terms. The approximate shadow molecular dynamics potential in combination with the extended Lagrangian formulation improves the numerical stability and reduces the number of Coulomb potential calculations required to evaluate accurate conservative forces. We demonstrate efficient and accurate simulations with excellent long-term stability of the molecular dynamics trajectories. The significance of choosing fixed or environment-dependent electronegativities and chemical hardness parameters is evaluated. Finally, we compute the infrared spectrum of molecules via the dipole autocorrelation function and compare to experiments to highlight the accuracy of the shadow molecular dynamics scheme with a machine learned flexible charge potential.

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:481959085
Book学术官方微信