From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Mon Aug 13 2007 - 09:16:09 CDT
Correction to the above email :
The CHARMM force fields however, do not yield the correct bilayer geometry
(area, thickness) .. WHEN THE NPT ensemble is used.
On 8/13/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
>
> 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
> > Schloss-Wolfsbrunnenweg 33
> > 69118 Heidelberg
> >
> > Tel: ++49-6221-533266
> > Fax: ++49-6221-533298
> >
> > e-mail:Vlad.Cojocaru[at]eml- r.villa-bosch.de
> >
> > http://projects.villa-bosch.de/mcm/people/cojocaru/
> >
> > ----------------------------------------------------------------------------
> >
> > EML Research gGmbH
> > Amtgericht Mannheim / HRB 337446
> > Managing Partner: Dr. h.c. Klaus Tschira
> > Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> > http://www.eml-r.org
> >
> > ----------------------------------------------------------------------------
> >
> >
> >
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
-- Maria G. Technical University of Denmark Copenhagen
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