[gmx-users] Simulated annealing

Marc Ceruso mceruso at physbio.mssm.edu
Wed Jul 30 21:10:01 CEST 2003

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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