VMD-L Mailing List

From: Ting Wang (twang_at_ucdavis.edu)
Date: Wed May 17 2006 - 13:52:21 CDT

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