From: David A. Case (
Date: Thu Mar 27 2008 - 16:35:11 CDT

On Tue, Mar 25, 2008, Krishnan, Marimuthu wrote:
> I would like to calculate reorientational time correlation function (second
> order Legendre polynomial form) of a bond vector (say, connecting atoms A
> and B). Is there a tcl script available for this purpose? I have written
> a fortran90 code for this but I have a feeling that vmd/tcl script can be
> efficient than my code! Since I am a newbie with VMD, I would appreciate if
> someone could help me in this. Thanks.

Since this doesn't have much to do with graphics or visualization, you might
consider a program like ptraj (see, which can process
Charmm or Amber trajectories, and compute the correlation functions in an
efficient manner (based on Fourier transforms). You can analyze multiple
bond vectors in a single pass through the trajectory.

Of course, that is no substitute for doing it yourself (from an educational

...good luck...dave case