[gmx-users] Dipolar correlation function

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 14 08:45:55 CET 2006

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 

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 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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