{"title":"通过路径规划生成的初始猜测,有效加快最小自由能路径的收敛速度","authors":"Yi Sun","doi":"10.1002/jcc.27504","DOIUrl":null,"url":null,"abstract":"<p>We demonstrate that combining a shifted clustering algorithm with a fast-marching-based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)-string combined approach), significantly reduces the number of iterations required for MEP convergence. This approach saves substantial time compared to using linear interpolation (LI) for the initial guess. Our method offers a viable solution for obtaining an effective initial guess of the MEP when an approximate or converged FEL is available. This work highlights the potential of applying FMT-based approaches to extract the MEP in chemical reactions.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27504","citationCount":"0","resultStr":"{\"title\":\"Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess\",\"authors\":\"Yi Sun\",\"doi\":\"10.1002/jcc.27504\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>We demonstrate that combining a shifted clustering algorithm with a fast-marching-based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)-string combined approach), significantly reduces the number of iterations required for MEP convergence. This approach saves substantial time compared to using linear interpolation (LI) for the initial guess. Our method offers a viable solution for obtaining an effective initial guess of the MEP when an approximate or converged FEL is available. This work highlights the potential of applying FMT-based approaches to extract the MEP in chemical reactions.</p>\",\"PeriodicalId\":188,\"journal\":{\"name\":\"Journal of Computational Chemistry\",\"volume\":\"46 1\",\"pages\":\"\"},\"PeriodicalIF\":3.4000,\"publicationDate\":\"2024-09-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27504\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Computational Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/jcc.27504\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/jcc.27504","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess
We demonstrate that combining a shifted clustering algorithm with a fast-marching-based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)-string combined approach), significantly reduces the number of iterations required for MEP convergence. This approach saves substantial time compared to using linear interpolation (LI) for the initial guess. Our method offers a viable solution for obtaining an effective initial guess of the MEP when an approximate or converged FEL is available. This work highlights the potential of applying FMT-based approaches to extract the MEP in chemical reactions.
期刊介绍:
This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.