VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Apr 24 2007 - 10:04:40 CDT

Hi Ignacio,
if you read the description associated with those scripts, you'll note
that it says you *must* have each molecule with a different number of
frames in a different file. This is because at the present time VMD (and
most similar programs) define a constant number of atoms for a molecule.
This is something that hopefully will be changing in the future because
there are currently a lot of simulation methodologies where this would
be helpful.

For now, you'll need to load them into separate files and then use the
script on that page, or the multimolanim plugin
(http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/), to view them.

Note that the reason your load is failing is that each of your xyz
files, on its own, only *has* one frame. If you delete the "first $i
last $i" it should work.

Peter

Ignacio Fernández Galván wrote:
> Hi all,
>
> I have a trajectory (actually, a set of configurations) in a xyz file,
> where the number of atoms in each structure is different, and I would
> like to display them in some kind of movie. According to this message
> (<http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3185.html>), I
> could load each structure in a separate molecule, but when I tried the
> scripts in this page
> (<http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect5>),
> with something like:
>
> for {set i 0} {$i < 15} {incr i} {
> mol new "file.xyz" first $i last $i
> }
>
> VMD didn't want to read the structures in frames after the first (it
> created molecules with 0 frames). Can it be made to work? I don't want
> to have each frame in a different file...
>
> Thanks a lot
>
>
> ___________________________________________________________
> Yahoo! Answers - Got a question? Someone out there knows the answer. Try it
> now.
> http://uk.answers.yahoo.com/
>