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!
--
========================================
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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