VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 11 2003 - 10:41:34 CST

Manuel,
  If the atoms are all of the same type, then yes, padding without preserving
order should work fine. You'll probably have to use the "dynamic bonds"
representation to make any sense of it as any bond information determined in
the first frame would be completely invalid in all subsequent frames if you
don't maintain the same ordering. If the atoms never bond with each other
at all, then its even simpler. :-)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 11, 2003 at 05:39:17PM +0100, Manuel Melle-Franco wrote:
> Dear John,
>
> Thanks for the prompt answer, and by the way nice program, :-).
>
> > At present VMD doesn't gracefully deal with trajectories containing
> > varying numbers of atoms. You could load each timestep as a separate
> Shame.
> > molecule and then animate them by toggling the molecules on/off with
> > a script, but this isn't nearly as nice as doing it the normal way.
> Hmmmm, interesting possibility.
>
>
> > If you try the "padding" trick you describe, you'll have to make sure
> > that the order of the atoms remains consistent from timestep to timestep.
> > Let us know if you need help getting one of these two techniques working.
>
> Unfortunately, in my case i am not just adding atoms, which will conserve the
> order, I am adding and deleting atoms so that the order cannot be conserved .
> The good side is that they are all the same kind of atom and with no
> connectivity at all, I wonder is this is enough to make it work even if the
> order is changing.
>
> Regards,
>
> Manuel
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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