http://folding.stanford.edu/English/FAQ-main#ntoc64
that the Graphical Client should show the potential energy of the current fold.
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The molecule drawn is the current atomic configuration ("fold") of the protein being simulated on your computer and the graph on the bottom shows the potential energy in femtosecond increments.
http://img690.imageshack.us/img690/1923 ... 2run66.jpg
I'm running FahCore_15.exe
I assume (question?) that the potential energy is a dynamic value over the time of a single folding session (work unit). And that the potential energy starts from some sizable positive value and then drives towards zero?
I think of GPU computation as a massively-parallel vector processor. And a MPVP is most obviously useful in terms of (large) matrix operations. Is there a FAQ somewhere that explains how F@H works at this level? (sort of: how is protein folding translated into matrix operations - and what operations of course?).