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Chinese Science Bulletin >>2011 >>56 >>(20)
Chinese Science Bulletin 2011, 56(20) 2114-2118 DOI: 10.1007/s11434-011-4543-7 ISSN: 1001-6538 CN: 11-1785/N
Application of the Mole-8.5 supercomputer: Probing the whole influenza virion at the atomic level
XU Ji1,2, WANG XiaoWei1, HE XianFeng1, REN Ying1*, GE Wei1*, LI JingHai1
1. State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China;
2. Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
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.
Keywords： influenza virion Mole-8.5 supercomputer GPU molecular dynamics simulation
Received 2011-03-18 Revised 2011-04-07 Online:
DOI: 10.1007/s11434-011-4543-7
Fund:
This work was supported by Ministry of Finance (ZDYZ2008-2), the National Key Science and Technology Project (2008ZX05014-003-006HZ), the Knowledge Innovation Project of Chinese Academy of Sciences (KGCX2-YW-124), and the National Natural Science Foundation of China (20821092).
Corresponding Authors: GE Wei
Email: yren@home.ipe.ac.cn; wge@home.ipe.ac.cn
http://csb.scichina.com:8080/kxtbe/EN/abstract/abstract503799.shtml
Chinese Science Bulletin 2011, 56(20) 2114-2118 DOI: 10.1007/s11434-011-4543-7 ISSN: 1001-6538 CN: 11-1785/N
Application of the Mole-8.5 supercomputer: Probing the whole influenza virion at the atomic level
XU Ji1,2, WANG XiaoWei1, HE XianFeng1, REN Ying1*, GE Wei1*, LI JingHai1
1. State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China;
2. Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
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.
Keywords： influenza virion Mole-8.5 supercomputer GPU molecular dynamics simulation
Received 2011-03-18 Revised 2011-04-07 Online:
DOI: 10.1007/s11434-011-4543-7
Fund:
This work was supported by Ministry of Finance (ZDYZ2008-2), the National Key Science and Technology Project (2008ZX05014-003-006HZ), the Knowledge Innovation Project of Chinese Academy of Sciences (KGCX2-YW-124), and the National Natural Science Foundation of China (20821092).
Corresponding Authors: GE Wei
Email: yren@home.ipe.ac.cn; wge@home.ipe.ac.cn
http://csb.scichina.com:8080/kxtbe/EN/abstract/abstract503799.shtml