VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 04 2006 - 22:46:01 CDT

Enzo,
  Yes, VMD currently requires that trajectories have a consistent
atom count for all frames. You can workaround this by creating
"dummy" atoms, but another issue you'll soon discover is that VMD
assumes a consistent structure (unchanging bonding pattern) from
one frame to the next, so that may also require special handling.
We plan to address this in future versions of the program, but this
is a limitation of the current design. Let me know if you need help
doing something with dummy atoms etc.

  John

On Mon, Sep 04, 2006 at 06:09:33PM +0200, Enzo Vitale wrote:
> Dear VMD people,
>
> I want to have a movie of a XYZ 'trajectory' file that I created by
> simply appending different individual trajectories.
> My problem is that later parts of the complete trajectory contain
> geometries with more atoms than the initial parts.
> In other words, I have a system which 'gains' atoms with time...
>
> Unfortunately VMD seems to treat this case too strictly, by sticking to
> the number of atoms in the initial frame.
> Is there any workaround for this problem ?
>
> Thanks in advance,
> Enzo 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078