[gmx-users] simulated annealing (SA)

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 24 13:29:58 CEST 2010

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.


> Thank you so much for any help!


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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