[gmx-users] area by lipid

[maite lopez cabezas]

Well I know that the x/y directions are scaled isotropically and the z
direction is scaled independiently, and i must give just 2
compresibility valors, but people don't give this valor in the most of
the papers about membrane simulations. For example i use
on  DPPC membrane
compressibility          =4.5e-5 4.5e-5
 ref-p                    = 1.0 1.0

the area change from 0.64 to 0.62. When i use the same parameter on
POPG or POPC bilayer  the system is exploding. If i change to
on POPC and POPG
compressibility          =1.0e-5  4.5e-5
 ref-p                    = 1.0 1.0

it gives areas about 0.639 (POPC) and 0.53 (POPG). The POPG area is
according to "Atomic-scale structure and electrostatics of anionic
POPG lipid bilayers with Na+ counterions", W. Zhao, T. Rog, A.A.
Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys J. 92, 1114-1124
(2007), and I'm using the same temperature. But the POPC area isn't
good.

My questions are:

Can i use  compressibility =0 4.5e-5 and  ref-p = 0 1.0 on
peptide-membrane systems? (at first the peptide is about 10 A to the
bilayer interface and after it's inserting in the membrane)

What are the correct valors for the compressibility on membrane systems?

Thanks a lot,

Maité


On Nov 24, 2007 10:27 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Hi:
> >
> > I am working on membrane simulation under lipid (DPPC, from Peter
> > Tieleman group site). I equilibrated dppc membrane for 10 ns and when
> > i got the area by lipid (x*y/ # lipids) using g_energy, i obtained
> > that the area is constant (0.64), there isn't any fluctuaction during
> > 10 ns..althougth the volumen isn't constant.
> > What's wrong in this simulation?
>
> Did you notice that your box dimensions are not changing in X and Y
> directions? Do you understand what semiisotropic pressure coupling does?
>
> Mark
>
>
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