[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.
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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