>Have you read the DE shaw 2010, 2011 science papers on folding?
Thanks for the pointer, highly interesting! This might complement what I'm thinking of.
>What are you looking at folding?
I would like to help with unknown structures of M.tuberculosis proteins, but participating
at CASP would be exciting too. I have other duties on the table atm, though.
Do you receive a huge speed-up from CUDA?
My reading is that it's at least 5-6x vs. quad core.
On a small protein <100 amino acids in a water box I could run maybe 1.5 nanoseconds a day.
You can probably speed that up by using a water sphere.
Ubiquitin in a water sphere (6,682 atoms) needs 16.12 seconds for 5 ps (2 fs steps),
that would be 26.8 nanoseconds/day on an AMD Phenom (6-core) and NVIDIA GTS 450.
You can get much better graphic cards now, however, the Tesla for example.
Try it yourself:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node8.html
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