[gmx-users] Dipolar correlation function

[chiradip chatterjee]

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 <spoel at xray.bmc.uu.se> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at 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
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 


Send instant messages to your online friends http://uk.messenger.yahoo.com