On Sun, Nov 20, 2011 at 8:19 PM, Dialing Pretty
The default value of the starting temperature of Phenix refine simulated annealing is 5000. At this temperature all the protein structure will be destroyed.
Will you please explain why we start the simulated annealing at 5000? Will you please explain to me the basic theory of the Phenix refine simulated annealing or tell me a link on the introduction of Phenix refine simulated annealing?
The method was developed by Axel Brunger in the late 1980s - these are good references: http://atbweb.stanford.edu/scripts/papers.php?sendfile=49 http://atbweb.stanford.edu/scripts/papers.php?sendfile=33 The annealing uses very few timesteps of dynamics (relative to a genuine MD simulation), so the protein doesn't have time to explode - but hopefully it will manage to escape local minima. The point isn't to be physically realistic anyway, just to optimize the fit to the X-ray data. -Nat