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Re: [modeller_usage] questions about model refinement protocol

On 7/4/10 11:48 AM, albert wrote:

I am reading Modeller9v8 manual and found in Page 14, 2.2.2, it is said
that models could be refined by VTFM with conjugated gradients(CG)
methods. In fact CG is usually applied to correct subtle errors and
steepest gradient (SG) is effective for some big erros. I am wondering
why not import SG for model refinement?
In fact, I found that may people would like to do SG before CG when they
are doing model refinement.
Conjugate gradients (CG) optimization is used in Modeller for local optimization, and refinement is done using simulated annealing with molecular dynamics, for global optimization. Steepest descents is not used, as CG typically can find the local minimum in fewer steps. 

	Ben Webb, Modeller Caretaker
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             http://www.salilab.org/modeller/
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