Application of the Mole-8.5 supercomputer:Probing the whole influenza virion at the atomic level

• 来源期刊: 科学通报(英文版)
• 学科: 生物学
• 年，卷（期）: 2011,（20）
• 页码范围: 2114-2118
• 页数: 5页
• 分类号: Q939.4
• 语种: 中文

摘要

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.