Efficient compressed database of equilibrated configurations of ring- linear polymer blends for MD simulations

K Hagita and T Murashima and M Ogino and M Omiya and K Ono and T Deguchi and H Jinnai and T Kawakatsu, SCIENTIFIC DATA, 9, 40 (2022).

DOI: 10.1038/s41597-022-01138-3

To effectively archive configuration data during molecular dynamics (MD) simulations of polymer systems, we present an efficient compression method with good numerical accuracy that preserves the topology of ring- linear polymer blends. To compress the fraction of floating-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 affect the numerical accuracy, then compressed the data with Huffman coding. We also provided a dataset of well- equilibrated configurations 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 10 9 MD steps to obtain 150 equilibrated configurations. The combination of JHPCN-DF and SZ compression achieved the best compression ratio for all cases. Therefore, the proposed method enables efficient 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.

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