{"title":"Implementation of the blue moon ensemble method","authors":"Y. Komeiji","doi":"10.1273/CBIJ.7.12","DOIUrl":null,"url":null,"abstract":"The blue moon ensemble method (Carter et al., 1989, Chem. Phys. Lett. 156, 472; Sprik & Ciccotti, 1998, J. Chem. Phys. 109, 7737) calculates the free energy profile of a chemical reaction along a specified reaction coordinate. The explicit algorithms for two simple reaction coordinates (“distance between two particles” and “difference between two distances”) are derived. The derived algorithms are presented by Fortran-like codes to facilitate their implementation in arbitrary programs.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"36 1","pages":"12-23"},"PeriodicalIF":0.4000,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"15","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chem-Bio Informatics Journal","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1273/CBIJ.7.12","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 15
Abstract
The blue moon ensemble method (Carter et al., 1989, Chem. Phys. Lett. 156, 472; Sprik & Ciccotti, 1998, J. Chem. Phys. 109, 7737) calculates the free energy profile of a chemical reaction along a specified reaction coordinate. The explicit algorithms for two simple reaction coordinates (“distance between two particles” and “difference between two distances”) are derived. The derived algorithms are presented by Fortran-like codes to facilitate their implementation in arbitrary programs.
blue moon ensemble method (Carter et al.， 1989, chemistry .)理论物理。左156,472;Sprik & Ciccotti, 1998, J. Chem。物理学报。109,7737)沿指定的反应坐标计算化学反应的自由能分布。推导了两个简单反应坐标(“两个粒子之间的距离”和“两个距离之间的差”)的显式算法。为了便于在任意程序中实现，所导出的算法采用了类似fortran的代码。
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