[gmx-users] auto coorelation function of a dipole

[Ruhong Zhou]

Hi,

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:

(See attached file: pair27-28.rotacf.eps)(See attached file:
pair27-28.acf.eps)

and here are the commands used:

% g_dipoles -P 2 -f full -s full -n pair27-28.ndx -c pair27-28.acf
% g_rotacf     -P 2 -f full -s full -n pair27-28.ndx -d -o pair27-28.rotacf

To be specific, I am baisically trying to calculate the ACF

   Cp(t) = \int P_2( cos \theta)
   cos \theta = p(t) \dot p(t+dt), then normalize
   P_2 (x) = (3x^2 -1)/2

Does anyone know what is going on here? The one from dipole autocorrelation
seems making more
sense....

Thanks.


Ruhong

Ruhong Zhou
IBM Thomas J. Watson Research Center
Route 134 & PO Box 218
Yorktown Heights,  NY 10598
Tel: (914) 945-3591, Fax: (914) 945-4104
http://www.research.ibm.com/people/r/ruhong



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