计算效率极化MD模拟:经典德鲁德振子极化力场的简单水模型

IF 4.8 2区 化学 Q2 CHEMISTRY, PHYSICAL
Xiaojing Teng, Wenbo Yu, Alexander D. MacKerell, Jr.
{"title":"计算效率极化MD模拟:经典德鲁德振子极化力场的简单水模型","authors":"Xiaojing Teng, Wenbo Yu, Alexander D. MacKerell, Jr.","doi":"10.1021/acs.jpclett.4c03451","DOIUrl":null,"url":null,"abstract":"An improvement in the computational efficiency of polarizable force field simulations is made through the development of a polarizable Drude water model, SWM3, in combination with the use of Lennard-Jones Particle Mesh Ewald (LJPME) for the treatment of long-range LJ interactions. The experimental bulk properties, density, heat of vaporization, dielectric constant, and self-diffusion constant of the SWM3 model are accurately replicated at ambient condition. The temperature dependence of the bulk properties is also captured except for the density. Microscopic properties, such as hydration free energy, dimer properties, and binding energies of clusters are well represented. The SWM3 model is ∼40% faster than the SWM4 water model traditionally used with the Drude force field, and use of LJPME offers an additional 30% speedup in heterogeneous systems. This combination makes the SWM3-based Drude model only 2.6-fold slower than the TIP3P-based additive simulations.","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":"137 1","pages":""},"PeriodicalIF":4.8000,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field\",\"authors\":\"Xiaojing Teng, Wenbo Yu, Alexander D. MacKerell, Jr.\",\"doi\":\"10.1021/acs.jpclett.4c03451\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"An improvement in the computational efficiency of polarizable force field simulations is made through the development of a polarizable Drude water model, SWM3, in combination with the use of Lennard-Jones Particle Mesh Ewald (LJPME) for the treatment of long-range LJ interactions. The experimental bulk properties, density, heat of vaporization, dielectric constant, and self-diffusion constant of the SWM3 model are accurately replicated at ambient condition. The temperature dependence of the bulk properties is also captured except for the density. Microscopic properties, such as hydration free energy, dimer properties, and binding energies of clusters are well represented. The SWM3 model is ∼40% faster than the SWM4 water model traditionally used with the Drude force field, and use of LJPME offers an additional 30% speedup in heterogeneous systems. This combination makes the SWM3-based Drude model only 2.6-fold slower than the TIP3P-based additive simulations.\",\"PeriodicalId\":62,\"journal\":{\"name\":\"The Journal of Physical Chemistry Letters\",\"volume\":\"137 1\",\"pages\":\"\"},\"PeriodicalIF\":4.8000,\"publicationDate\":\"2025-01-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"The Journal of Physical Chemistry Letters\",\"FirstCategoryId\":\"1\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jpclett.4c03451\",\"RegionNum\":2,\"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":"The Journal of Physical Chemistry Letters","FirstCategoryId":"1","ListUrlMain":"https://doi.org/10.1021/acs.jpclett.4c03451","RegionNum":2,"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

通过开发极化Drude水模型SWM3,结合使用Lennard-Jones粒子网格Ewald (LJPME)来处理远程LJ相互作用,提高了极化力场模拟的计算效率。SWM3模型的实验体积特性、密度、汽化热、介电常数和自扩散常数在环境条件下得到了精确的复制。除了密度外,还捕获了体积特性的温度依赖性。微观性质,如水化自由能、二聚体性质和团簇的结合能得到很好的表现。SWM3模型比传统上使用Drude力场的SWM4水模型快约40%,LJPME的使用在异质系统中提供了额外30%的加速。这种组合使得基于swm3的Drude模型仅比基于tip3p的添加剂模拟慢2.6倍。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field

Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field
An improvement in the computational efficiency of polarizable force field simulations is made through the development of a polarizable Drude water model, SWM3, in combination with the use of Lennard-Jones Particle Mesh Ewald (LJPME) for the treatment of long-range LJ interactions. The experimental bulk properties, density, heat of vaporization, dielectric constant, and self-diffusion constant of the SWM3 model are accurately replicated at ambient condition. The temperature dependence of the bulk properties is also captured except for the density. Microscopic properties, such as hydration free energy, dimer properties, and binding energies of clusters are well represented. The SWM3 model is ∼40% faster than the SWM4 water model traditionally used with the Drude force field, and use of LJPME offers an additional 30% speedup in heterogeneous systems. This combination makes the SWM3-based Drude model only 2.6-fold slower than the TIP3P-based additive simulations.
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
The Journal of Physical Chemistry Letters
The Journal of Physical Chemistry Letters CHEMISTRY, PHYSICAL-NANOSCIENCE & NANOTECHNOLOGY
CiteScore
9.60
自引率
7.00%
发文量
1519
审稿时长
1.6 months
期刊介绍: The Journal of Physical Chemistry (JPC) Letters is devoted to reporting new and original experimental and theoretical basic research of interest to physical chemists, biophysical chemists, chemical physicists, physicists, material scientists, and engineers. An important criterion for acceptance is that the paper reports a significant scientific advance and/or physical insight such that rapid publication is essential. Two issues of JPC Letters are published each month.
×
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