Re: bilayer thickness in simulation of POPC membranes

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Mon Aug 13 2007 - 07:55:48 CDT

Hi Vlad,

I cannot answer your questions completely, but you might want to be aware of
the following:

- The thickness (or area) of a lipid bilayer in atomistic simulations (even
with united atom force fields) is known to equilibrate over 10s of ns (see
recent papers from Tieleman or Vattulainen). So, in the first place, do not
expect your bilayer to be equilibrated in 1.6 ns.

- I am not aware in detail of the force field that you have used to run the
simulations. The CHARMM force fields however, do not yield the correct
bilayer geometry (area, thickness). See the following article
Jensen et. al. Biophys. J. 2004 86: 3556-3575**

Hope this helps,

-Maria

On 8/10/07, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>
> Dear NAMD, VMD users,
>
> I performed some simulations with a solvated POPC membrane created in
> VMD (100/100 A2 - total 274 lipids). Simulations were performed in NAMD.
> I applied 1.6 ns of equilibration in NPT ensemble (Langevin dynamics for
> T control and Langevin Piston for P control) using flexible cell. The
> force field is a united atom force field with RESP charges as described
> by Lin, Baker, and McCammon (Biophysical Journal, 2004). Amber topology
> file was used.The periodic cell looks as nicely equilibrated with an
> arrea per lipid of 68.3 (close to the experimental value) ...
>
> However, I have some problems with the thickness of the bilayer which
> seems much smaller than it should be. When I meassure the thickness
> considering the phosphates, I get a value around 27 A which seems to be
> much lower than both the value reported experimentally (37 A) and the
> startuing value in the VMD built membrane. In the 2004 BJ paper, Justin
> G et al reported a thickness of ~ 35 A, also calculated considering the
> phosphates as far as I understood.
>
> Did anybody observed such a behavior ? If yes, could somebody give me a
> hint why this happens ?
>
> Now, I have to say that in my equilibration I didint apply the 1 phase
> of keeping only the headgroups fixed and heat the system to 500 K to
> "melt" the hydrophobic core .... Instead, I have an intital phase of
> keeping the entire membrane fixed and gradually release the constraints
> ... Could this be the problem ??
>
> Thanks for answering
>
> Best
> vlad
>
>
> --
>
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
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>
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>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
>
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-- 
Maria G.
Technical University of Denmark
Copenhagen

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