[gmx-users] auto coorelation function of a dipole

[David]

On Sat, 2002-11-02 at 07:14, Ruhong Zhou wrote:
> 
> I am trying to calculate the ACF of a N-H dipole in a protein (BPTI,
> residue ASP3, N-H atom pair).
> >From the manual, it seems I can use both g_rotacf and g_dipoles. However,
> the auto correlation
> frunctions from g_rotacf and g_dipole are very different. Here are the two
> eps files:

g_dipoles works on molecules, not on individual vectors. Your index is
interpreted as molecule indices, probably water in this case.
If you do a fit as you see probably do in g_rotacf you should get the
right numbers. Do you have any idea what kind of order parameters to
expect? It seems that the correlation function has not leveled out
anyway.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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