Application of Deconvolution in Path Integral Simulations

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Ádám Madarász, Gergely Laczkó
{"title":"Application of Deconvolution in Path Integral Simulations","authors":"Ádám Madarász, Gergely Laczkó","doi":"10.1021/acs.jctc.4c00564","DOIUrl":null,"url":null,"abstract":"In path integral molecular dynamics (PIMD) simulations, atoms are represented by several replicas connected with harmonic springs, so additional vibrations appear beyond the physical vibrations because of the normal mode frequencies coming from the springs of the ring polymer. In harmonic approximation, the frequencies of these internal modes can be determined exactly from the physical frequencies. We show that this formal effect of the path integral simulations on the vibrations can be considered as a convolution if we use the square of the frequency as an independent variable. This convolution can be represented as a matrix multiplication. The potential of the formalism is demonstrated in two applications. We present an alternative method to determine the power spectrum of thermostats used in PIMD simulations. We also show that in simple anharmonic model systems, the physical frequencies can be obtained from ring polymer molecular dynamics simulations by deconvolution, even in cases where spurious resonances appear.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7000,"publicationDate":"2024-10-15","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.4c00564","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

Abstract

In path integral molecular dynamics (PIMD) simulations, atoms are represented by several replicas connected with harmonic springs, so additional vibrations appear beyond the physical vibrations because of the normal mode frequencies coming from the springs of the ring polymer. In harmonic approximation, the frequencies of these internal modes can be determined exactly from the physical frequencies. We show that this formal effect of the path integral simulations on the vibrations can be considered as a convolution if we use the square of the frequency as an independent variable. This convolution can be represented as a matrix multiplication. The potential of the formalism is demonstrated in two applications. We present an alternative method to determine the power spectrum of thermostats used in PIMD simulations. We also show that in simple anharmonic model systems, the physical frequencies can be obtained from ring polymer molecular dynamics simulations by deconvolution, even in cases where spurious resonances appear.

Abstract Image

路径积分模拟中的解卷积应用
在路径积分分子动力学(PIMD)模拟中,原子由多个用谐波弹簧连接的复制品表示,因此,由于来自环状聚合物弹簧的正常模态频率,会出现物理振动之外的额外振动。在谐波近似中,这些内部模态的频率可以根据物理频率精确确定。我们表明,如果使用频率的平方作为自变量,路径积分模拟对振动的这种形式上的影响可视为一种卷积。这种卷积可表示为矩阵乘法。我们在两个应用中展示了这一形式主义的潜力。我们提出了另一种方法来确定 PIMD 模拟中使用的恒温器的功率谱。我们还展示了在简单的非谐波模型系统中,即使在出现假共振的情况下,也可以通过解卷积从环状聚合物分子动力学模拟中获得物理频率。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
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