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Supercomputer Performs Simulation of Virus
moller writes to tell us Red Herring is reporting that researchers from the University of California at Irvine and the University of Illinois at Urbana-Champaign have announced that they created a computer simulation of a virus. From the article: "Using one of the world's fastest computers at the U.S. National Center for Supercomputing Applications, located at the University of Illinois at Urbana-Champaign, the researchers ran a computer program devised to reverse engineer the dynamics of all atoms making up the virus particle and a tiny drop of water containing it." Nature also has an interesting write up on the research surrounding this project.
1. The full research page for this project is here. This is a lot better than the stuff linked through Nature and such.
2. The image was actually generated by our group, and specifically Anton Arkhipov, using our software package VMD. NCSA didn't have anything to do with it.
Also of note: we've done a series of cluster-building workshops specifically focusing on the software and hardware required to run these kinds of simulations. Copies of the presentations and tutorials are linked off of that page.
And if you want to see how we designed our clusters, I've got full specifications up here.
In order to get the more "trustable" simulations to produce something in the ballpark of remotely representing reality, you have to know "the answer" before you do the simulation and then teach the model to reproduce that "answer"... then you can write a paper and show that you're model "get's the answer" - and that's about the limit of "insight" that's often gained from these sort of simulations.
You are, of course, absolutely right. Things haven't changed since I started to do this kind a long time (20 years) ago. However, you can gain some sort of insights, as you can find out which interactions (even thought they are simplified) can matter in the real world. By trying to simulate the real world, you can find out more about it, even if you aren't able to make many predictions.