By Rob Mitchum // March 4, 2014
The HIV virus is 60 times smaller than a red blood cell, but it’s still a massive problem for scientists. From the perspective of atomic modeling, one tiny virus is equivalent to millions of atoms — a quantity that’s far too high to simulate with today’s most powerful supercomputers. So to study HIV and other important biological and chemical molecules, scientists at the CI’s Center for Multiscale Theory and Simulation have turned to a simpler approach: coarse-grained modeling. Instead of simulating the influence of physics upon every single atom in a molecule, coarse-grained modeling groups atoms together to allow for a balance of scientific precision and computational feasibility.
In a new feature at the website of the National Center for Supercomputing Applications, writer Trish Barker looks at how CMTS director Gregory Voth and postdoctoral researcher John Grime adapted coarse-grained modeling for use on NCSA’s petascale Blue Waters supercomputer.
“What we did was decide not only to do the coarse-grained but also to combine it with extreme-scale computing and push the limits of what people can do,” Voth says.
To accomplish this, postdoctoral researcher John Grime developed an entirely new coarse-grained molecular dynamics code specifically designed for extreme-scale computing systems that harness the power of hundreds of thousands of processors.
“We weren’t following any existing prescription, we weren’t copying something. There was no textbook answer,” says Grime. “It was liberating.”
Read the rest of the article here, and find out more about how Grime used coarse-grained modeling to simulate HIV’s suit of armor.