Supercomputer simulates H1N1 virus

A team from the Institute of Process Engineering of Chinese Academy of Sciences (CAS-IPE) is using Nvidia Tesla gpus to create the world's first computer simulation of a whole H1N1 influenza virus at the atomic level. Using the Mole-8.5 gpu accelerated supercomputer, which uses more than 2200 Nvidia Tesla gpus, the researchers generated molecular dynamics simulation as a 'computational microscope' to peer into the atomic structure of the virus. Currently, it is difficult to study bacteria and viruses in laboratory experiments as reactions are often too fast to capture. Computer simulations had previously been beyond the reach of supercomputers due to the complexity of simulating billions of particles with the right environmental conditions. The CAS-IPE researchers made the simulation breakthrough by developing a molecular dynamics simulation application that takes advantage of gpu acceleration. It was run on the Mole-8.5 gpu supercomputer, which is comprised of 288 server nodes. The system was able to simulate 770 picoseconds per day with an integration time step of 1 femtosecond for 300million atoms. Dr Ying Ren, assistant professor at CAS-IPE, said: "The Mole-8.5 gpu supercomputer is enabling us to perform scientific research that simply was not possible before. This research is an important step in developing more effective ways to control epidemics and create anti-viral drugs."