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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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