VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed May 17 2006 - 14:21:55 CDT

This problem is most likely due to the straightness of the tails
initially. If you start a simulation with the entire membrane free
to move, the tails will interdigitate very easily, thus making it
harder for them to randomize (and as a result, reducing the bilayer
thickness). However, if you first simulate for a short time (up to
0.5 ns) with the headgroups fixed, the tails will "melt", adopting a
more natural configuration.

This paper discusses in more detail some of the complexities of
simulating lipid bilayers:

Justin Gullingsrud and Klaus Schulten. Lipid bilayer pressure
profiles and mechanosensitive channel gating. Biophysical Journal,
86:3496-3509, 2004.

On May 17, 2006, at 1:52 PM, 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