From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 27 2008 - 17:08:08 CDT

Hi,
  Yes, 'ptraj' can take care of many of these tasks quite well.
One can often use VMD to convert between file formats to make it possible
to mix and match analysis tools from AMBER, GROMACS, CHARMM, and other
programs. Whenever practical I would always recommend people try using the
analysis tools that are already out there. If the tools that are out there
don't yet do exactly what you want, you can always contribute new code.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 27, 2008 at 02:35:11PM -0700, David A. Case wrote:
> 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

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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