VMD-L Mailing List

From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Wed Nov 09 2011 - 16:38:39 CST

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
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16854.html
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: sam.wallace_at_adelaide.edu.au
"I suppose you wouldn't have a problem with me saying the fermi-dirac
distribution is a soup kitchen"