[gmx-users] simulated annealing (SA)

[Justin A. Lemkul]

shahab shariati wrote:
> Hi all
>  
> I have some questions about simulated annealing (SA):
>  
> 1) Is SA a optimization method? or a minimization method?
>  

It is probably best described as optimization.

> 2) Steps in md simulation are as follow:
>  
> (a) minimization (b) equilibration (c) production run (d) analysis
>  
> so, where do SA  lie in previous line? (before or after minimization)
>  

Minimization should probably always be your first step.  If you subject a 
non-minimized structure to temperature fluctuations in SA, then the whole thing 
will probably just collapse, depending on what you're doing during the SA protocol.

-Justin

>  
> Thank you so much for any help!
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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