[gmx-users] Dipolar correlation function

[David van der Spoel]

chiradip chatterjee wrote:
> Hi gmx user,
> Is there any way in gromacs to compute dipolar
> correlation function between solvent atom and one atom
> of my protein from trajectory data? I went through
> g_rotacf with -d option. But I think it gives 
> rotational correlation function for linear molecules
> by specifying two atoms (i,j) in the index file that
> means two atoms i-j with a bond.
> Is g_dipole -corr is an option?
> please advice me.
> Chiradip
> 
Please be more specific, what do you want to compute? Please give an 
equation.

g_dipoles -corr computes a dipole vector from given atoms (e.g. a water 
molecule) and computes it's rotational autocorrelation.

g_rotacf may do what you need, you don't need a bond, just a vector 
between two atoms. However, if they diffuse apart more than half a box 
periodic boundary conditions will kick in and give strange results...

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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