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.
Pseudo-particle modeling （PPM）, a molecular modeling method which combines time-driven algorithms and hard molecule modeling, was originally developed for simulating gas in complex multiphase systems （Ge ＆ Li, 2003; Ge et al., 2005; Ge, 1998）. In this work, the properties of two- and three-dimensional pseudo-particle systems, namely, mean free path, compressibility factor, self-diffusion coefficient and shear viscosity, are systematically measured by using PPM. it is found that in terms of an effective diameter, the results well conform to the Chapman-Enskog theory, thus suggesting that PPM can be employed to simulate the micro- and meso-scale behavior of ordinary gas and fluid flows.
