[gmx-users] area by lipid

[Alan Dodd]

----- Original Message ----
From: maite lopez cabezas <lopezmai at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, November 25, 2007 10:48:31 AM
Subject: Re: [gmx-users] area by lipid

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.

-> Is that the POPG where they observe a permanent hydrogen bond between the mid-OH of the glycerol, and the phosphate?

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)

-> Not unless you *intend* the membrane to be unable to expand or contract.  This is what gave you zero variability before.  Compressibility of zero means your box will not compress (or expand) in that dimension.  If you're adding peptides, I'd imagine true NPT is important.  Personally, I use a surface tension (XY pressure not equal to 1) to artificially fix the area/lipid.  This still has issues, of course...

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

-> People don't tend to specify in their papers, unfortunately.  I've always gone for using the water value, as it'll be in the right ballpark and I don't believe it's too critical.

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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