VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 24 2005 - 14:22:45 CST

Hi,
  I'd suggest taking a look at Jan Saam's PBCWrap script, it
should be able to do much of what you want, and could certainly
be modified to do more if it doesn't have all of the features you're
looking for:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 21, 2005 at 09:44:07PM -0800, Vani Krishna wrote:
>
> Dear VMD users:
>
> I have a question regarding the wrapped version of DCd
> files and rewriting them. I have a configuration for
> the system, which was run by NAMD with 'wrap ON'.
> Unfortunately towards the end of the system run, the
> wrapping has really distorted my system (e.g, water in
> between lipid head groups!). I want to make a movie
> out of this, but it really looks ugly with things
> jumping in and out of the box and also analysis is
> kind of hard this way.
>
> Is there any script out there that i can use in VMD,
> where I can choose the center of the box and wrap it
> and write a new DCD?
>
> Thanks
> Vani
>
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-- 
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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