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

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. © 2011 Science China Press and Springer-Verlag Berlin Heidelberg.