[gmx-users] pressure coupling for lipid bilayer
periole at inka.mssm.edu
Thu May 2 20:17:14 CEST 2002
Erik Lindahl wrote:
> >Yes, the lipid forcefield parameters should reproduce all the properties
> >of the membrane. But because, in the case of the surface area, the limitation
> >in size of the patch you can simulate introduces a systematic scrinckage
> >of your lateral box dimension (ref: SE Feller and RW Pastor, Biophysical J.,
> >1996 vol 71 p 1350), you have to apply a surface tension that rectify this.
> >The forcefield is not the problem, the size of the system is the problem.
> Both Scott (Feller) and Rick (Pastor) are nice guys and very good
> scientist, but I think
> most membrane people now agree that the argument in the above article is
> NOT valid.
> There are small finite size effects on bilayers (We've simulated from 64
> to 1024 lipids, see
> Biophysical Journal, 79, 426 (2000)), but we're talking about 1-2 nm^2
> per lipid here, never
> 10 nm^2 per lipid.
You mean A^2, right !! The difference I observe depending on the size
of the patch is almost less 4 A^2, for POPC, from 72 to 288 lipids.
It's a little more than what you observed in the paper you mentioned.
I know it very well by the way.
Don't get me wrong. I am not saying that parameters are perfect. But
I think that saying there is no or negligible effect in patch size is going
way to far for me. The area/lipid is one think, but the order parameter
is depending on it (cause/consequence whatever) and it's effect on the
protein membrane function, activity is well recognize now, so I consider
that the area/lipid has to be well reprocduce, for this kind of simulations.
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