Guest post from Profs Kasson and Shirts, UVA and Mr. Coffland
new version of Gromacs (4.6) is coming, and we’re working to bring it
to Folding@home. The new code contains a number of improvements (more
than you’d expect for a minor version number!), and we’ll post about
some of the individual features as we go. Not all of them will be
available on F@h immediately, as some will require substantial
development work over the next few months. But some of the basics are
new free energy methods from our very own Prof. Michael Shirts, new and
slightly faster inner-loop code, and some important tweaks to
parallelization. Free energy calculations allow us to calculate things
like how tightly drugs bind to proteins and the strength of attraction
between protein components when pulled apart. And you, of course, know
what faster inner-loop code and better parallelization mean!
Gromacs is an interesting piece of simulation software in that it’s heavily optimized both for single-computer performance (part of why we chose it for F@h in the first place) and for parallel scaling. A lot of codes choose to emphasize one or the other. But Gromacs tries to do both. That will have some interesting and useful implications for F@h particularly as we look at more and more cores on donor CPU’s (and things like GPU integration). That’s all for now; we’ll keep you posted on progress.
The 4.6 Core Team (Profs. Kasson, Shirts, and the indefatigable Mr. Coffland)