M. Sekijima, J. Doi, S. Honda, T. Noguchi, S. Shimizu, Y. Akiyama
{"title":"Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation","authors":"M. Sekijima, J. Doi, S. Honda, T. Noguchi, S. Shimizu, Y. Akiyama","doi":"10.2197/IPSJDC.3.757","DOIUrl":null,"url":null,"abstract":"We created a Free Energy Landscape Analysis System based on a parallelized molecular dynamics (MD) simulation adapted for the IBM Blue Gene/L supercomputer. We begin with an outline of our Free Energy Landscape Analysis system. Next we discuss how Parallel MD was tuned for Blue Gene/L. We then show the results for some test targets run on Blue Gene/L, including their efficiency. Finally, we mention some future directions for extension of this project.","PeriodicalId":432390,"journal":{"name":"Ipsj Digital Courier","volume":"30 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2007-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Ipsj Digital Courier","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.2197/IPSJDC.3.757","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
We created a Free Energy Landscape Analysis System based on a parallelized molecular dynamics (MD) simulation adapted for the IBM Blue Gene/L supercomputer. We begin with an outline of our Free Energy Landscape Analysis system. Next we discuss how Parallel MD was tuned for Blue Gene/L. We then show the results for some test targets run on Blue Gene/L, including their efficiency. Finally, we mention some future directions for extension of this project.
我们创建了一个基于并行分子动力学(MD)模拟的自由能景观分析系统，该系统适用于IBM Blue Gene/L超级计算机。我们首先概述我们的自由能景观分析系统。接下来我们讨论平行MD是如何为蓝色基因/L调整的。然后我们展示了在Blue Gene/L上运行的一些测试目标的结果，包括它们的效率。最后，提出了本项目未来的扩展方向。
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