Re: bilayer thickness in simulation of POPC membranes

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Mon Aug 13 2007 - 10:00:10 CDT

Vlad,

I had the same problem with POPE. Equillibrate the membrane with the Z
positions constrained.

Best,

Ilya

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
>
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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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-- 
Ilya Chorny Ph.D.

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