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Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer

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Abstract

Evaluation of effective coarse graining (CG) degree and reasonable speedup relative to all-atomistic (AA) model was conducted to provide a basis for building appropriate larger-scale model. The reproducibility of atomistic conformation and temperature transferability both act as the analysis criteria to resolve the maximum acceptable CG degree. Taking short- and long time spans into account simultaneously in the estimation of computational speedup, a dynamic scaling factor is accessible in fitting mean squared displacement ratio of CG to AA as an exponential function. Computing loss in parallel running is an indispensable component in acceleration, which was also added in the evaluation. Subsequently, a quantified prediction of CG speedup arises as a multiplication of dynamic scaling factor, computing loss, time step, and the square of reduction in the number of degrees of freedom. Polyethylene oxide was adopted as a reference system to execute the direct Boltzmann inversion and iterative Boltzmann inversion. Bonded and non-bonded potentials were calculated in CG models with 1~4 monomers per bead. The effective CG degree was determined as two at the most with a speedup of four orders magnitude over AA in this study. Determination of effectiveness CG degree and the corresponding speedup prediction provide available tools in larger spatiotemporal-scale calculations.

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Acknowledgments

The parallel computing was supported by the National Supercomputing Center in Shenzhen (Shenzhen Cloud Computing Center) and the Computing Facility, Institute of Mechanics, Chinese Academy of Sciences.

Funding

This study was funded by the National Natural Science Foundation of China (Project No. 11672314).

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Authors and Affiliations

  1. Key Laboratory for Mechanics in Fluid Solid Coupling Systems, Institute of Mechanics, Chinese Academy of Sciences, No.15, Beisihuan West Road, Haidian District, Beijing, 100190, People’s Republic of China

    Lijuan Liao, Changyu Meng & Chenguang Huang

  2. School of Engineering Science, University of Chinese Academy of Sciences, No.19(A), Yuquan Road, Shijingshan District, Beijing, 100049, China

    Changyu Meng & Chenguang Huang

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  1. Lijuan Liao
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  2. Changyu Meng
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  3. Chenguang Huang
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Contributions

Conceptualization: Lijuan Liao; Methodology: Lijuan Liao and Changyu Meng; Formal analysis and investigation: Lijuan Liao and Changyu Meng; Writing—original draft preparation: Lijuan Liao; Funding acquisition: Lijuan Liao; Supervision: Chenguang Huang.

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Correspondence to Lijuan Liao.

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Liao, L., Meng, C. & Huang, C. Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer. J Mol Model 27, 55 (2021). https://doi.org/10.1007/s00894-020-04661-5

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