Abstract
Compared with gene research, human proteomics research is relatively rare. There is less research, that is protein dynamic structure in the cross-disciplinary field. For precision medicine, proteomics research is necessary. This article starts with software and aims to speed up the protein simulation process and reduce the experimental cycle. In order to reduce the time-consuming of protein simulation and non-biopolymer simulation process and improve the performance of GROMACS software. This paper optimized the performance of GROMACS by using manual vectorization to optimize its hotspots on Sunway TaihuLight System, and designed several test cases. The experiment was simulated and evaluated for performance testing. The final optimization effect is remarkable, reaching a speedup ratio of about 136%.
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Acknowledgements
This research is jointly supported by the Science and Technology Support Program of Sichuan Province (Grant NO. 2017JQ0030). The authors also thank the reviewers for their time and efforts during the review process.
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Tang, X., Wu, T., Wang, T., Wu, J. (2019). Molecular Dynamics Simulation Optimization Based on GROMACS on Sunway TaihuLight. In: Sun, X., Pan, Z., Bertino, E. (eds) Artificial Intelligence and Security. ICAIS 2019. Lecture Notes in Computer Science(), vol 11633. Springer, Cham. https://doi.org/10.1007/978-3-030-24265-7_10
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DOI: https://doi.org/10.1007/978-3-030-24265-7_10
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