[gmx-users] Simulated annealing
kay.gottschalk at weizmann.ac.il
Wed Jul 30 21:27:00 CEST 2003
If you really want SA, try the program CNS - it has a nice SA
implementation, although you'd have to do the calculations in vacuo
first, I'd guess. After the SA in Vacuo (as a minimization...) you
could switch to Gromacs and do a free simulation in water.
On Wednesday, July 30, 2003, at 10:23 PM, 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
>>> 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
>>> and look at the trajectory !! It should convice you. But I don't
>>> know if
>>> it is relevant for your problem.
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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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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
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