[gmx-users] Simulated annealing 10000K
kay.gottschalk at weizmann.ac.il
Thu Jul 31 16:00:01 CEST 2003
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:
> 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
> that the peptide does have a unique stable conformation the search for
> would be to find a protocol/forcefield that would accurately determine
> 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
> (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
> of convergence.
> I hope this helps
> On Thu, 31 Jul 2003, Osmany
> Guirola Cruz wrote:
> i have 10 simulations , i do g_cluster to each one and then i do
> 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
> 9 ? ? ? ? ? ? ?
> 10 0.269739 0.224798 0.375789 0.433382 0.349531 0.403248
> 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
> that was the problem in my simulation at 1000K my
> ten final structures are quite diferent after the
> Xavier Periole wrote:
> Yop, sorry I meant 1000 K. 10000 K is way too
> 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
> 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.
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Tel: ++972-8-9343639
> Herzl St. 1
> Rehovot 76100
> _______________________________________________ gmx-users mailing list
> gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Size: 5237 bytes
Desc: not available
More information about the gromacs.org_gmx-users