Details, please?
Can you give me a link to the relevant parts of the Folding@Home website?
(Solvent effects have always been the bane of protein simulations.)
Cheers!
F@H uses the TINKER and GROMACS core to fold proteins, and there are other newer cores available to use.
From the High Performance FAQ at Stanford U:
Why push for new technologies, such as GPUs or the PS3, rather than try to recruit more CPU clients?
In order to tackle many of the problems of interest (especially related to protein misfolding and aggregation, such as in Alzheimer's Disease), we need to not just have lots of computers participating, but we need results returned more quickly so that we can simulate trajectories of sufficient length. Right now, we achieve this by running for many months to years (indeed, our first Alzheimer's Disease simulations ran for almost two years straight). That's where the new clients come in. They give us considerably longer trajectories in the same wall clock time, allowing us to turn what used to take years to simulate even on FAH, to a few weeks to months.
What types of calculations do the new clients speed?
There are primarily two types of calculations we perform, which differ by how we simulate water. The GPU and PS3 clients greatly speed "implicit solvation" simulations, in which water is handled mathematically in a continuum fashion (see the Wikipedia article on implicit solvation for more information). Our SMP client will significantly speed "explicit solvent" simulations, where water atoms are handled atom by atom, in an explicit fashion, just like any other atom in our system. Currently, the GPU & PS3 only significantly speed implicit solvation and the SMP client only speeds explicit solvent, so each has its limits, but together they work to give FAH considerably more computational power than ever before.
Links cited above:
WikiAlso, you could ping Dan Ensign over at the F@H Forum.
F@H is one of the very few DC projects where you can ping the actual developers, and even the PhD in charge, Vijay Pande, and get answers.
Check out this link. If you see something interesting, ping Dan. He is terrific in replying quickly.
http://forum.folding-community.org/ftopic14500.html