[gmx-users] Fourier transformations of protein motions

David spoel at xray.bmc.uu.se
Sat May 10 13:48:00 CEST 2003

On Sat, 2003-05-10 at 13:30, Ing. Vojtěch Spiwok wrote:
> Hallo all GROMACS people
> I would like to ask about some tool to perform an analysis of
> protein motions by fourier transform to get power spectra
> (intensity of motion vs. frequency) possibly for each atom,
> residue or owerall spectra for protein. I would like also ask
> about compatibility of such analysis with LINC, SHAKE,
> temperature coupling and other MD details.
That could be interesting. The question is what you are interested in.
If you put in harmonic bonds you will see them in your spectra, at
frequencies corresponding to the force constants. If that is what you
want you have to turn off constraints and simulate with a very short
timestep. If you want to see slower motions, you can turn on the
constraints and use normal 2 fs time step. You could also consider
trying the essential dynamics and normal mode analyses, which are
stadard techniques, and could be a good reference point for analysis.

> Cheers
> Vojtech Spiwok
> Biochemistry and Microbiology@
> ICT Prague
> Czech Republic
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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