VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 17 2006 - 13:59:01 CDT

Ting,
  I'm not really the person to ask about building membranes.
I'm a computer scientist, not a biophysicist. :-)

You could ask Ilya Balabin (author of the membrane plugin):
  http://www.chem.duke.edu/~ilya/

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 17, 2006 at 11:52:21AM -0700, Ting Wang wrote:
> Dear John,
>
> Thanks for your reply.
>
> Here I have another question about the lipid bilayer constructed in VMD.
>
> There is overlap between the legs of the two lipids from each layer. This
> results in a thickness of ca. 37A for the POPC lipid bilayer . But after
> MD simulations, the overlap becomes much more and the thickness is only
> 27-29A. Is this the right thickness value?
>
> I noticed that there is no leg overleap in the initial structure of the
> lipid bilayer constructed differently by other people (e.g. Peter Tieleman)
> and 37A is the equilibrated thickness.
>
> Thanks!
>
> Ting
>
>
> ----- Original Message -----
> From: "John Stone" <johns_at_ks.uiuc.edu>
> To: "Ting Wang" <twang_at_ucdavis.edu>
> Cc: <vmd-l_at_ks.uiuc.edu>
> Sent: Monday, May 15, 2006 10:33 AM
> Subject: Re: vmd-l: bug in membrane plugin
>
>
> >
> >Hi,
> > I hadn't heard about this previously, I'll have to have a look
> >and see what's going on there. Not much has changed with that plugin
> >since Ilya originally wrote it, so hopefully this is easy to fix.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, May 11, 2006 at 11:47:11AM -0700, Ting Wang wrote:
> >>
> >>Dear VMD users,
> >>
> >>It seems there is a bug in the Membrane Plugin.
> >>
> >>When the membrane size is larger than 50A x 50A, the commond "membrane -l
> >>popc ..." will generate lipid molecules with serious clash. Some
> >>atom-atom
> >>distances are even smaller than 0.2A.Energy minimization can not get over
> >>it, actually minimiztion can not run.
> >>
> >>Did anybody else notice this? Can this bug be fixed?
> >>
> >>Thank you very much!
> >>
> >>Ting
> >
> >--
> >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 

-- 
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