[gmx-users] Simulated annealing

[David]

On Wed, 2003-07-30 at 23:43, 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
> :-( . 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. ???????  
> 
I wouldn't use SA in this case, but rather simulated the peptides in
solvent (each of the ten with exactly the same number of solvent
molecules and box size) and then first let it relax and then do a short
free simulation to measure the energy (Epot including solvent). Your
lowest energy is the most likely structure, although the forcefield can
be wrong.


> 
> 
> 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
> >  
> >  
> 
> _______________________________________________ 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.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++