bilayer thickness in simulation of POPC membranes

From: Vlad Cojocaru (
Date: Fri Aug 10 2007 - 10:56:41 CDT

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


Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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