VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 19 2005 - 15:05:17 CDT

Hi,
  If you've lost molecules to the far reaches of empty space and
the simulation isn't using periodic boundary conditions, then you're
just going to have to scale down the molecule and crank up the
far clip plane to something large. Try reducing the size by 10:
  scale by 0.1

If this is the result of a simulation using periodic boundary conditions,
you will probably want to use something like PBCWrap to do coordinate
wrapping when fragments cross the periodic boundary:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

Without more information about your simulation, it's hard to give more
specific suggestions.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 18, 2005 at 04:11:45PM -0400, Margaret Shun Cheung wrote:
> Dear VMD wizards,
>
> I had a md simulations and molecules slowly drifted away, disappeard from
> the screen. I tried to adjust Near clip to 0 and far clip to 30, but
> still can't prevent such trajedy.... Please help. Thank you.
>
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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