高性能计算的应用:Born-Oppenheimer水溶液中复杂形成的分子动力学

M. Khrenova, D. Kapusta, I. V. Babchuk, Yulia I. Meteleshko
{"title":"高性能计算的应用:Born-Oppenheimer水溶液中复杂形成的分子动力学","authors":"M. Khrenova, D. Kapusta, I. V. Babchuk, Yulia I. Meteleshko","doi":"10.14529/jsfi180312","DOIUrl":null,"url":null,"abstract":"The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 10 times for Cs and Na ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.","PeriodicalId":338883,"journal":{"name":"Supercomput. Front. Innov.","volume":"19 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"4","resultStr":"{\"title\":\"Applications of High Performance Computing: Born-Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions\",\"authors\":\"M. Khrenova, D. Kapusta, I. V. Babchuk, Yulia I. Meteleshko\",\"doi\":\"10.14529/jsfi180312\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 10 times for Cs and Na ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.\",\"PeriodicalId\":338883,\"journal\":{\"name\":\"Supercomput. Front. Innov.\",\"volume\":\"19 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2018-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"4\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Supercomput. Front. Innov.\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.14529/jsfi180312\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Supercomput. Front. Innov.","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.14529/jsfi180312","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 4

摘要

超级计算机技术的进步促进了计算化学方法及其应用的发展,特别是从头算势的分子动力学模拟。这些新方法可以解决重要的化学和技术问题。特别是,溶剂萃取和分离技术被广泛用于减少放射性废物的数量,特别是存在于液相中的放射性铯同位素。我们证明了Cs和Na离子在碱阳离子和杯[4]芳烃之间的结合常数的计算值相差10倍,这与实验值吻合得很好。我们报告了929个原子组成的模型系统的基准计算结果,该模型是用具有经验色散校正D3的gga型泛函PBE和高斯函数与具有Goedecker-Teter-Hutter伪势的平面波DZVP的组合基在密度泛函理论近似中描述的。我们证明,如果在Lomonosov-2超级计算机上节点数量为16,计算效率将下降到一半左右。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Applications of High Performance Computing: Born-Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions
The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 10 times for Cs and Na ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.
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
自引率
0.00%
发文量
0
×
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