Hi David Thanks for your reply. I want to calculate dipolar corelation function C(t) between proton and fluorine using the equation:
C(t) = 1/4Σ[(3cos2θ(0)-1 )(3cos2θ(t)-1 )]/r(0)r3(t) (ref Fellar et al, JACS 121, 8963-64, 1999) where I have a proton i and total n fluorines. At time = 0, a proton-fluorine vector has a length r(0) and is oriented at an angle θ(0) relative to the z-axis. At a time t later in the trajectory the vector has length r(t) and is oriented at an angle θ(t) relative to the z-axis. Is there any way to get the plot of the average C(t) vs time (ps)? Thanks in advance Chiradip --- David van der Spoel <[EMAIL PROTECTED]> wrote: > 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 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Send instant messages to your online friends http://uk.messenger.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
