[gmx-users] Simulated annealing

[David]

On Thu, 2003-07-31 at 00:30, Osmany Guirola Cruz wrote:
> Ok, David, but for generate my box i do:
> 1- editconf -f p.gro -o p.gro -bt cubic -c -d 0.7
> 2- genbox -cp p.gro -cs spc216.gro -o p.gro -p p.top
> my peptides have diferent structure , and then my BOX 
> and my number of H2O are diferent, my question is.
> hOW COULD I GENERATE  exactly the same number of solvent 
> molecules and box size.
> thanks

take the smallest number of any you get from genbox, and take away
molecules manually from the other ones.

> 
> 
> 
> David wrote:
> > 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
> > > >  
> > > > 
> > > >       
> > > 
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> > >     
> 
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-- 
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
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