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