VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 19 2005 - 18:42:53 CDT

Hi,
  You will probably want to ask this question of Ilya Balabin,
the original author of the membrane plugin:
  http://fds.duke.edu/db/aas/Chemistry/post%2520docs/ilya.balabin

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 15, 2005 at 11:20:56AM -0500, Meyer, Douglas K (UMC-Student) wrote:
> To anyone who can help,
> I am a student in the Physics Department of the University of Missouri Columbia. I am working with a small group in a BioPhysics class and could use some help.
>
> We are working with a protein channel called GramicidinA. We are imbedding this channel into a lipid bilayer and manipulating it in different ways. My problem is this.
>
> When using the membrane plugin, the only parameters I seem to be able to change are the membrane tyep (POPE in our case) and the x and y dimensions of the membrane. Is there anyway that I can make the water added on both sides of the system deeper? Having larger water baths on either side seems to be what we need to work on an additional problem. I would greatly appreciate any help. Thanks again
>
> Doug Meyer 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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