{"title":"利用集合重权重和电位对比,根据实验数据优化力场。","authors":"Xinqiang Ding*, ","doi":"10.1021/acs.jpcb.4c02147","DOIUrl":null,"url":null,"abstract":"<p >Despite force field improvements over the past decades, we still encounter situations where simulation results disagree with experiments due to force field inaccuracies. Such situations provide opportunities to improve force fields. In this study, we introduce a novel framework for optimizing force fields using experimental data. The unique feature of this framework is that it aims to optimize force fields to match experiments while minimizing the perturbation made to the original force field. To achieve this, we combine ensemble reweighting techniques with the potential contrasting method. Ensemble reweighting is used to reweight an ensemble of conformations generated using an existing force field to match experimental data while minimizing the perturbation to the original ensemble. Potential contrasting is then utilized to optimize force field parameters to reproduce the reweighted ensemble. We demonstrate the framework’s effectiveness by optimizing a coarse-grained force field for intrinsically disordered proteins using experimental radius of gyration data.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8000,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting\",\"authors\":\"Xinqiang Ding*, \",\"doi\":\"10.1021/acs.jpcb.4c02147\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p >Despite force field improvements over the past decades, we still encounter situations where simulation results disagree with experiments due to force field inaccuracies. Such situations provide opportunities to improve force fields. In this study, we introduce a novel framework for optimizing force fields using experimental data. The unique feature of this framework is that it aims to optimize force fields to match experiments while minimizing the perturbation made to the original force field. To achieve this, we combine ensemble reweighting techniques with the potential contrasting method. Ensemble reweighting is used to reweight an ensemble of conformations generated using an existing force field to match experimental data while minimizing the perturbation to the original ensemble. Potential contrasting is then utilized to optimize force field parameters to reproduce the reweighted ensemble. We demonstrate the framework’s effectiveness by optimizing a coarse-grained force field for intrinsically disordered proteins using experimental radius of gyration data.</p>\",\"PeriodicalId\":60,\"journal\":{\"name\":\"The Journal of Physical Chemistry B\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2024-07-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"The Journal of Physical Chemistry B\",\"FirstCategoryId\":\"1\",\"ListUrlMain\":\"https://pubs.acs.org/doi/10.1021/acs.jpcb.4c02147\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"The Journal of Physical Chemistry B","FirstCategoryId":"1","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acs.jpcb.4c02147","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting
Despite force field improvements over the past decades, we still encounter situations where simulation results disagree with experiments due to force field inaccuracies. Such situations provide opportunities to improve force fields. In this study, we introduce a novel framework for optimizing force fields using experimental data. The unique feature of this framework is that it aims to optimize force fields to match experiments while minimizing the perturbation made to the original force field. To achieve this, we combine ensemble reweighting techniques with the potential contrasting method. Ensemble reweighting is used to reweight an ensemble of conformations generated using an existing force field to match experimental data while minimizing the perturbation to the original ensemble. Potential contrasting is then utilized to optimize force field parameters to reproduce the reweighted ensemble. We demonstrate the framework’s effectiveness by optimizing a coarse-grained force field for intrinsically disordered proteins using experimental radius of gyration data.
期刊介绍:
An essential criterion for acceptance of research articles in the journal is that they provide new physical insight. Please refer to the New Physical Insights virtual issue on what constitutes new physical insight. Manuscripts that are essentially reporting data or applications of data are, in general, not suitable for publication in JPC B.