• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

一种基于格拉斯曼流形上密度矩阵外推的准时间可逆格式用于玻恩-奥本海默分子动力学

A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born-Oppenheimer Molecular Dynamics.

作者信息

Pes Federica, Polack Étienne, Mazzeo Patrizia, Dusson Geneviève, Stamm Benjamin, Lipparini Filippo

机构信息

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.

CERMICS, École des Ponts and Inria Paris, 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Valée, France.

出版信息

J Phys Chem Lett. 2023 Nov 2;14(43):9720-9726. doi: 10.1021/acs.jpclett.3c02098. Epub 2023 Oct 25.

DOI:10.1021/acs.jpclett.3c02098
PMID:37879072
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10626629/
Abstract

This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in Born-Oppenheimer Molecular Dynamics (BOMD) simulations. The method shows excellent results on four large molecular systems that are representative of real-life production applications, ranging from 21 to 94 atoms simulated with Kohn-Sham (KS) density functional theory surrounded with a classical environment with 6k to 16k atoms. Namely, it clearly reduces the number of self-consistent field iterations while at the same time achieving energy-conserving simulations, resulting in a considerable speed-up of BOMD simulations even when tight convergence of the KS equations is required.

摘要

本信函介绍了一种基于密度矩阵格拉斯曼外推法的所谓准时间可逆方案(QTR G-Ext),用于在玻恩-奥本海默分子动力学(BOMD)模拟中精确计算初始猜测值。该方法在四个大型分子系统上展现出优异的结果,这些系统代表了实际生产应用,从21个原子到94个原子,采用含时密度泛函理论(KS)进行模拟,并处于由6k至16k个原子组成的经典环境中。具体而言,它显著减少了自洽场迭代次数,同时实现了能量守恒模拟,即使在需要严格收敛KS方程的情况下,也能大幅加速BOMD模拟。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/116d/10626629/a32d316b4042/jz3c02098_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/116d/10626629/11ea1398e754/jz3c02098_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/116d/10626629/a32d316b4042/jz3c02098_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/116d/10626629/11ea1398e754/jz3c02098_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/116d/10626629/a32d316b4042/jz3c02098_0002.jpg

相似文献

1
A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born-Oppenheimer Molecular Dynamics.一种基于格拉斯曼流形上密度矩阵外推的准时间可逆格式用于玻恩-奥本海默分子动力学
J Phys Chem Lett. 2023 Nov 2;14(43):9720-9726. doi: 10.1021/acs.jpclett.3c02098. Epub 2023 Oct 25.
2
Grassmann Extrapolation of Density Matrices for Born-Oppenheimer Molecular Dynamics.用于玻恩-奥本海默分子动力学的密度矩阵格拉斯曼外推法
J Chem Theory Comput. 2021 Nov 9;17(11):6965-6973. doi: 10.1021/acs.jctc.1c00751. Epub 2021 Oct 8.
3
On the existence of the optimal order for wavefunction extrapolation in Born-Oppenheimer molecular dynamics.关于玻恩-奥本海默分子动力学中波函数外推最优阶数的存在性
J Chem Phys. 2016 Jun 28;144(24):244103. doi: 10.1063/1.4954234.
4
Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.含耗散的 Born-Oppenheimer 分子动力学的拉格朗日表述,采用密度泛函紧束缚方法。
J Chem Phys. 2011 Jul 28;135(4):044122. doi: 10.1063/1.3605303.
5
An extrapolation method for the efficient calculation of molecular response properties within Born-Oppenheimer molecular dynamics.一种在 Born-Oppenheimer 分子动力学中高效计算分子响应性质的外推方法。
Phys Chem Chem Phys. 2013 Jun 21;15(23):9392-6. doi: 10.1039/c3cp50204j. Epub 2013 May 10.
6
Efficient, "On-the-Fly", Born-Oppenheimer and Car-Parrinello-type Dynamics with Coupled Cluster Accuracy through Fragment Based Electronic Structure.基于片段的电子结构实现高效、“即时”、玻恩-奥本海默和 Car-Parrinello 型动力学与耦合簇精度。
J Chem Theory Comput. 2017 May 9;13(5):1887-1901. doi: 10.1021/acs.jctc.6b01107. Epub 2017 Apr 13.
7
Next generation extended Lagrangian first principles molecular dynamics.下一代扩展拉格朗日第一性原理分子动力学。
J Chem Phys. 2017 Aug 7;147(5):054103. doi: 10.1063/1.4985893.
8
Car-Parrinello Monitor for More Robust Born-Oppenheimer Molecular Dynamics.用于更稳健的玻恩-奥本海默分子动力学的卡-帕里尼罗监测器
J Chem Theory Comput. 2019 Aug 13;15(8):4454-4467. doi: 10.1021/acs.jctc.9b00439. Epub 2019 Aug 1.
9
Accelerated, energy-conserving Born-Oppenheimer molecular dynamics via Fock matrix extrapolation.通过福克矩阵外推实现的加速节能玻恩-奥本海默分子动力学
Phys Chem Chem Phys. 2005 Sep 21;7(18):3269-75. doi: 10.1039/b509494a. Epub 2005 Aug 12.
10
Generating accurate density matrices on the tangent space of a Grassmann manifold.在格拉斯曼流形的切空间上生成精确的密度矩阵。
J Chem Phys. 2023 Feb 7;158(5):051101. doi: 10.1063/5.0137775.

本文引用的文献

1
Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation.半经验阴影分子动力学:PyTorch 实现。
J Chem Theory Comput. 2023 Jun 13;19(11):3209-3222. doi: 10.1021/acs.jctc.3c00234. Epub 2023 May 10.
2
Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor.快速方法研究复杂体系中的激发态动力学及其在利用黄素光受体进行蓝光光解中的应用。
J Phys Chem Lett. 2023 Feb 9;14(5):1222-1229. doi: 10.1021/acs.jpclett.2c03797. Epub 2023 Jan 30.
3
From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain.
从晶体学数据到光感受器的溶液结构:以AppA蓝光感应结构域为例
Chem Sci. 2021 Sep 9;12(40):13331-13342. doi: 10.1039/d1sc03000k. eCollection 2021 Oct 20.
4
Grassmann Extrapolation of Density Matrices for Born-Oppenheimer Molecular Dynamics.用于玻恩-奥本海默分子动力学的密度矩阵格拉斯曼外推法
J Chem Theory Comput. 2021 Nov 9;17(11):6965-6973. doi: 10.1021/acs.jctc.1c00751. Epub 2021 Oct 8.
5
Molecular Mechanisms of Activation in the Orange Carotenoid Protein Revealed by Molecular Dynamics.分子动力学揭示橙色类胡萝卜素蛋白激活的分子机制。
J Am Chem Soc. 2020 Dec 30;142(52):21829-21841. doi: 10.1021/jacs.0c10461. Epub 2020 Dec 17.
6
Excited state Born-Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA.通过含时密度泛函理论和 AMOEBA 耦合的激发态 Born-Oppenheimer 分子动力学。
Phys Chem Chem Phys. 2020 Sep 16;22(35):19532-19541. doi: 10.1039/d0cp03688a.
7
Density-Matrix Based Extended Lagrangian Born-Oppenheimer Molecular Dynamics.基于密度矩阵的扩展拉格朗日玻恩-奥本海默分子动力学
J Chem Theory Comput. 2020 Jun 9;16(6):3628-3640. doi: 10.1021/acs.jctc.0c00264. Epub 2020 May 21.
8
Extended Lagrangian Born-Oppenheimer molecular dynamics using a Krylov subspace approximation.使用克里洛夫子空间近似的扩展拉格朗日玻恩-奥本海默分子动力学
J Chem Phys. 2020 Mar 14;152(10):104103. doi: 10.1063/1.5143270.
9
Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.迈向具有先进点偶极可极化嵌入的复杂系统的大规模混合量子力学/分子力学动力学。
Chem Sci. 2019 Jun 11;10(30):7200-7211. doi: 10.1039/c9sc01745c. eCollection 2019 Aug 14.
10
Tinker 8: Software Tools for Molecular Design.Tinker 8:分子设计软件工具。
J Chem Theory Comput. 2018 Oct 9;14(10):5273-5289. doi: 10.1021/acs.jctc.8b00529. Epub 2018 Sep 19.