Re: [modeller_usage] SA IN optimize.py

[Modeller Caretaker <modeller-care@ucsf.edu>]

vidhya sankar wrote:
> i would like to implement *simulated anealing* protocol in *optimize.py 
> <http://optimize.py/> script*.along with default optimization

If by 'optimize.py' you mean the script given at 
http://salilab.org/modeller/9v2/manual/node250.html then implementing 
simulated annealing is simple - it's just several calls to md.optimize() 
at progressively lower temperatures.

If you mean for automodel model optimization, simulated annealing is 
already done. You can change the SA protocol by tweaking 
automodel.md_level; see http://salilab.org/modeller/9v2/manual/node46.html

	Ben Webb, Modeller Caretaker
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