VMD-L Mailing List

From: David A. Case (case_at_scripps.edu)
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 http://ambermd.org), 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
standpoint).

...good luck...dave case