[gmx-users] Simulated annealing 10000K

[Kay Gottschalk]

I'd do much more than ten structures. Do as many as you can in a 
reasonable time and afterwards cluster the results! You cannot expect 
your system to converge so easily...
On Thursday, July 31, 2003, at 02:00 AM, Osmany Guirola Cruz wrote:

> that was the problem in my simulation at 1000K my ten final structures 
> are quite diferent after the SA.
>
> Xavier Periole wrote:
>
>
>
>
>
>  
>  
> Yop, sorry I meant 1000 K. 10000 K is way too much.
>  
> Marco is right. With 11 residues it is unlikely that your peptide has 
> a unique
> conformation in solvent. It probably explore different conformations 
> with diffenrent
> probabilities.
>  
> How did you generate your 10 structures with Modeler. I thought it 
> needed a
> template !! And what isthe point of doing an SA on a specific 
> conformation ?
> You loose it at 1000K anyway !!
> I did some thing similar where I generated 100 conf from SA with an 
> implicit
> solvent (faster) and after that I made clusters of them.
>  
> XAvier
>  
>
>
>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel
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