[gmx-users] auto coorelation function of a dipole

David spoel at xray.bmc.uu.se
Sun Nov 3 23:35:06 CET 2002

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

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

More information about the gromacs.org_gmx-users mailing list