[jaydee]

All you can do is sit it out. It sucks hardcore. I had one comp stuck for 12hrs once. The client will only use a maximum of 150megs of RAM so that shouldn't be to much of an issue. The best thing to do is get as much mhz out of your system as possible. The good news is there is a thing called the laxness levels. If you get stuck the lax levels rise and the next steps go by a lot faster.

Bah, better then my half ass explaination here is a quote from the Phase 2 FAQ

My protein keeps getting stuck. Is my computer broken?
The new software uses a different approach to compute protein structures from phase I, (except for generation 0). Structure are computed by perturbing ever so slightly the best structure from the previous generation. Due to this restriction, there are a lot less places the protein can 'go' at each step and it is a lot more likely to bump into other atoms while building.

To counter this, the algorithm will 'give up' after a certain number of attempts (up to several hundred thousand in some cases) and start building the structure from the beginning again, in the hopes of avoiding the sticky point. If it continually gets stuck however, it will slowly increase the structure laxness levels. A given stuck structure will give up and restart folding after making 25N(log10 N)*CUBRT(gen)*SQRT(R) tries to place a residue, where N is the number of residues in the protein, gen the current generation number (or 1 for generation zero), and R is the residue number currently being placed. On a fast (2 GHz) computer this equates to 2-3 minutes real-time for a typical protein.

The structure laxness levels are three numbers which affect the quality of structures generated - basically how serious of an atomic clash is allowed and so on. The higher these get, the poorer the quality of the structure that gets built (in terms of geometry) but the less likely it will get stuck. Hence if you just leave it alone when stuck, it will eventually raise these laxness levels high enough to get unstuck. The levels are raised very slowly (for obvious reasons), however, the good news is, once raised, they maintain their levels so that you are not likely to get stuck again for nearly as long as the very first time it gets stuck. At the end of a generation the laxness levels are just slightly decreased, but will increase again if it gets stuck for awhile.

Thus getting stuck with this new algorithm is perfectly normal and to be expected, and although it may appear your computer is doing nothing, it is actually trying literally millions of placements trying to get all the atoms to fit together. Although it may still for several hours on one generation, once it gets through it, the others are not likely to take nearly as long, so do not get discouraged. We encourage everyone to let the client run and get up to generation 250, as that is where all the scientifically interesting stuff will begin to happen.