VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 03 2010 - 14:46:34 CDT

Hi,
  VMD is currently designed such that it is assumed that atom counts
and atomic element do not change over the course of simulation. This
allows VMD to significantly optimize various graphics and analysis
operations by taking advantage of this. If you want to load simulations
like you describe into VMD, you will need to load each of the frames as
a separate molecule, and then use the "multimolanim" plugin to animate
them etc.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

 
On Mon, May 03, 2010 at 10:10:58AM -0400, Maxim Paliy. wrote:
> Dear VMD experts.
>
> What is the best way to produce an animation, where
> the number of atoms and their names change between the frames?
>
> I try to read the frames from a multi-frame pdb or xyz files that I
> make in my simulation.
>
> However, it seems, VMD gets the idea about the number and the names of
> atoms present
> from the FIRST frame only.
>
> is the there a way to change this?
>
> Thanks a lot in advance for any suggestions,
> Maxim 

-- 
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