[gmx-users] g_chi again!!!

David spoel at xray.bmc.uu.se
Wed Feb 19 21:52:43 CET 2003

On Wed, 2003-02-19 at 18:14, ehab at biof.ufrj.br wrote:
> Hi people,
> Me and my friend Alan wrote before,trying to use g_chi. Then you recommended us 
> to use the g_chi2 version. But we yet don't find how to calculate the 
> transitions of sidechains angles as a function of time with g_chi. Wich options 
> should I use to calculate de transitions?

g_chi -all gives you all dihedral angles as a function of time.

The problem is determining what a transition is ... One way is the
dihedral autocorrelation function, which in the limit of long
simulations will give you an estimate of the transition time. In
proteins it may of course be infinite (on the MD time scale)

> Thanks in advance,
> Elza
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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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