[gmx-users] Simulated annealing

[Kay Gottschalk]

It might very well be that your system is way to flexible; you'd need 
experimental (=NMR) restraints, I'd guess. Even a cyclic hexapeptide is 
very flexible and basically improbable to predict correctly.

On Thursday, July 31, 2003, at 01:15 AM, Osmany Guirola Cruz wrote:

> my peptide have 11 aminoacids and it is cyclic.
>
> Marc Ceruso wrote:
>
> On Wed, 30 Jul 2003, Osmany Guirola Cruz wrote:
>
>
>
> Thanks again Xavier,
> I have this problem:
> I have a peptide whit unknown structure, whit "modeler" i  get 10
> diferents structures of my peptide, and then.....
> i use SA whith the ten models to obtain a "superminimized structure" 
> but
> my final structures are NOT similar
>
>
> How long is the peptide? Why do you think that your structures should 
> be
> similar? In any case, if the peptide is small let's say 1-40 amino 
> acids
> chances are that its structure in solution is not unique, but in any 
> case
> the similiraty within your ensemble will depend on the strength of the
> restraints used to generate the structures. If the homology of your
> peptide/protein is low the constraints will be loose reflecting the 
> lack
> of empirical knowlege regarding your sequence, in others reflecting the
> uncertainty in the structure.
>
>
>
>
>
> :-( . i have the idea that my simulations converge to a unique 
> structure
> (my SA = "1000K" to 300K) you say 10 000 i will probe
> with 10000 to see what happens. ???????
>
>
>
> Xavier Periole wrote:
>
> I guess you have been reading papers from NMR procedures to
> generate their models corresponding to the data. If that what you
> are doing It would be easier to get a program that NMR people
> use, is is probably implemented
> It seeems difficult to do that automatically in gromacs, at least
> for me.
> I guess you that could modify the strength of the constant on the
> angles
> and bonds in the parameter file and do that for each temperature
> you
> need but that's gonna to be a pain in the ...
> I don't know what you are doing but I can assure you that at 10000
> K
> the system is pretty flexible. Try to simulate it for 10 ps at
> 10000 K
> and look at the trajectory !! It should convice you. But I don't
> know if
> it is relevant for your problem.
>
> XAvier
>
>
>
>
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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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