From: John Stone (
Date: Fri Nov 11 2011 - 10:06:58 CST

  At present, there really isn't a good way to "expand" an existing
trajectory by adding new particles to it, at least not within VMD or
by using catdcd. You could write some code to do this however if
you're handy. Other than writing some special code, I don't have
a better suggestion at this moment. Maybe someone else has an idea
besides writing custom code.

  John Stone

On Thu, Nov 10, 2011 at 09:08:39AM +1030, Sam Wallace wrote:
> Hi
> I'm trying to create a tcl script to measure a radial distribution
> function from the centre of mass of an arbitrary selection.
> I've read through the mailing list and this message seemed the most helpful
> in particular this part
> >method b): you create a fake molecule that contains
> >only one atom per solute but the rest as is and then
> >write a script that copies over the coordinates and
> >replaces the coordinates for the one solute atom
> >per molecule with the center of mass of the whole
> >molecule. that would be a bit time consuming, but
> >not very complicated if you build this script step by
> >step.
> If I'm understanding this method correctly, it would require modifying
> the input structures and running the simulations again. What I'm
> hoping to do is modify the existing trajectories
> I've made a script that will create a new molecule with 1 atom, and
> the same number of frames as the original trajectory, and it then sets
> the position of that atom to the centre of mass of an arbitrary
> selection over the trajectory.
> I've looked at the TopoTools plugin and the mergemols procress, but it
> only handles single frames.
> So my question(s) are.
> 1) Is there some simple function or method of adding a dummy atom to
> an existing trajectory?
> 2) Is there a method to merge the atoms of two trajectories together?
> Thanks,
> -Sam
> --------------------------------------------------------------
> Sam Wallace, Ph.D Student
> School of Chemistry and Physics, University of Adelaide
> Adelaide, South Australia 5005, Australia
> Phone: +61-(0)8-8303-4332
> Fax: +61-(0)8-8303-4358
> Email:
> "I suppose you wouldn't have a problem with me saying the fermi-dirac
> distribution is a soup kitchen"

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