[gmx-users] Simulated annealing 10000K

[Kay Gottschalk]

To be honest,  I think that will not work. You will probably have to 
deal with ensembles of probable (=low-energy) structures. To get decent 
ensembles, you need much more than 10 structures. If you heat up the 
structures to 1000K, the start conformation shouldn't be that important 
any more. I'd calculate on the order of 100 or more conformations and 
see whether or not I can detect any clusters.

On Thursday, July 31, 2003, at 07:53 PM, Osmany Guirola Cruz wrote:

> Thanks Marc
> But if i have 10 diferent structures for the same peptide and  i heat 
> it to 1000K and then cool it to 300K
> to each one , i supose that my 10 final structures must be similar. My 
> idea was to find a unique structure for my peptides
> an then do MD.
>
>
> Marc Ceruso wrote:
>
> Hi-
>  Your results are not surprizing. But it seems to me that you would be
> happier if you had one single structure for you peptide. Even if it 
> were
> that the peptide does have a unique stable conformation the search for 
> it
> would be to find a protocol/forcefield that would accurately determine 
> the
> correct fold of your peptide: protein folding problem. However, small
> peptides do not have a unique
> structure in solution. Numerous NMR studies on many peptides have shown
> that the peptides (in general) are in  equilibirium between different
> forms. Take a look at the enkephalin (Scheraga) studies, or some of 
> Ernst
> (NMR) studies.
> If you have experimental data on your peptide, You could run classical
> MD simulations (see Daura and van Gunsteren) for a very long time
> (tens/hundreds of ns)and  evaluate
> your computational results against the NMR data. That would be the 
> measure
> of convergence.
> I hope this helps
> Marco
>
>
>
>   On Thu, 31 Jul 2003, Osmany
> Guirola Cruz wrote:
>
>
>
> i have 10 simulations , i do g_cluster to each one and then i do 
> g_confrm
> whith the most populated clusters
> and , these is the table:
>
>          1                  2                 3                4
>          5                 6               7                    8
> 9        10
>  1      *
>  2  0.255333      *
>  3  0.384980  0.268161      *
>  4  0.363748  0.356637  0.312702      *
>  5  0.364454  0.291378  0.168395  0.360910      *
>  6  0.304329  0.362637  0.352839  0.224768  0.350295      *
>  7  0.395214  0.427625  0.373925  0.340693  0.329041  0.264797      *
>  8  0.395720  0.347483  0.315446  0.462918  0.295911  0.384215  
> 0.404703
>  9     ?          ?         ?         ?         ?         ?         ?
> 10  0.269739  0.224798  0.375789  0.433382  0.349531  0.403248  
> 0.452217
> 0.382978
>
>
>
>
> Kay Gottschalk wrote:
>       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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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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