[phenixbb] a question on starting temperature of Phenix refine simulated annealing

[Nathaniel Echols]

On Sun, Nov 20, 2011 at 8:19 PM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> 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