文章基本信息

标题：Efficient compressed database of equilibrated configurations of ring-linear polymer blends for MD simulations
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作者：Katsumi Hagita ; Takahiro Murashima ; Masao Ogino 等
期刊名称：Scientific Data
电子版ISSN：2052-4463
出版年度：2022
卷号：9
期号：1
页码：1-9
DOI：10.1038/s41597-022-01138-3
语种：English
出版社：Nature Publishing Group
摘要：To efectively archive confguration data during molecular dynamics (MD) simulations of polymer systems, we present an efcient compression method with good numerical accuracy that preserves the topology of ring-linear polymer blends . To compress the fraction of foating-point data, we used the Jointed Hierarchical Precision Compression Number - Data Format (JHPCN-DF) method to apply zero padding for the tailing fraction bits, which did not afect the numerical accuracy, then compressed the data with Hufman coding . We also provided a dataset of well-equilibrated confgurations of MD simulations for ring-linear polymer blends with various lengths of linear and ring polymers, including ring complexes composed of multiple rings such as polycatenane . We executed 109 MD steps to obtain 150 equilibrated confgurations . The combination of JHPCN-DF and SZ compression achieved the best compression ratio for all cases . Therefore, the proposed method enables efcient archiving of MD trajectories . Moreover, the publicly available dataset of ring-linear polymer blends can be employed for studies of mathematical methods, including topology analysis and data compression, as well as MD simulations .