Application of the Mole-8.5 supercomputer: Probing the whole influenza virion at the atomic level |
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Authors: | Ji Xu XiaoWei Wang XianFeng He Ying Ren Wei Ge JingHai Li |
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Institution: | (1) Key Laboratory of Computer System and Architecture, Chinese Academy of Sciences, Beijing, 100190, China;(2) Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China;(3) Graduate University of Chinese Academy of Sciences, Beijing, 100049, China |
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Abstract: | Discrete computer simulations are quite helpful in understanding dynamic structures in complex systems. Recently, using the
Mole-8.5 supercomputer and molecular dynamics simulations as a “computational microscope”, we simulated the dynamic structure
of a whole H1N1 influenza virion in solution for the first time at the atomic level. In total, 300 million atoms in a periodic
cube with an edge length of 148.5 nm were simulated. Using 288 low level hybrids with 1728 C2050 GPUs and a software package
developed specifically for the hardware, the simulation executed 770 ps/d with an integration time step of 1 fs, and analyzed
the dynamic structure. With the tremendous computational power of GPUs, efficient software packages for various hardware designs,
and consistent physical models, more challenging applications will be carried out in the near future. |
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Keywords: | influenza virion Mole-8 5 supercomputer GPU molecular dynamics simulation |
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