From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 06 2006 - 13:19:08 CDT

Hi,
  If you're doing a periodic simulation, your structure may be wrapping
across the periodic boundaries as the trajectory plays back. You could
fix this by applying cancelling out any center of mass motions with a script,
or you could go further and use the RMSD Trajectory Tool extension to align
the frames to a reference frame. In both cases you'll probably have
to make sure your using unwrapped atom coordinates, otherwise you'll have
other problems.
  
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 05, 2006 at 01:35:41AM -0400, Dongsheng Zhang wrote:
> Dear VMD users,
>
>
> I would like to visualize my protein's trajectory without water (there
> is water in my simulation, but I remove them before running vmd). I
> found my protein will jump around, even out of the window. Is there any
> way to prevent it (in other words, center my protein in the window in
> every frame)? Does anyone has the script if a script can does the job?
>
>
> Thank you!
>
>
> Dongsheng

-- 
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
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