[gmx-users] pressure coupling for lipid bilayer
Shang-Te Danny Hsu
hsu at nmr.chem.uu.nl
Thu May 2 11:01:45 CEST 2002
>>There has been some discussions about proper pressure coupling for lipid
>>bilayer. My experience is that the anisotropic or semiisotropic coupling
>>with compressibility of 6e-5 or 4.5e-5 along the membrane normal easily
>>deforms the bilayer in < 20ps and eventually the bilayer is flattened!!
> 20 ps for a lipid simulation is nothing. The deformation can be due to
> a relaxation, fluctuation ....
It is totally flat like a smashed sandwich!! So something must be wrong
about my setting!
>>On the other hand, with isotropic or without any P-coupling, the system
>>is running quite well.
> Isotropic is ideally the one we should use because real but in nature !!
> We are making simulations where not differencing the lateral and normal
> pressure is probably not good idea. It works for some of us. Depends mostly
> in the problem you are addressing.
What I'd like to monitor is the pore formation mechanism and this is important to have a proper membrane definition!!
> Using a surface tension is often necessary to reproduce the surface area
> (per lipid) determine experimentally for most (if not all) of the known
> In your case, POPC, the experimental value of the surface area per lipid is
> well known. Values vary from 72 A*A to 62 A*A (at 50 d Celsius), which
> makes a big difference in surface tension to apply.
> I used/use semi-isotropic with POPC with the default compressibility. I
> Areas ranging from 51 to 69 A*A depending in the conditions of the
> (paper to come). The only common point of all the simulations I have done
> is that
> the equilibration is long (2-5 ns), and depends of how far you are from the
> equilibrium value which complitly reflect the condiitons you choose.
> hope it'll serve you
It might be a trivial question, but how do you determine the surface area per lipid?
What I used is by "g_sas" (solvent accessible surface) to calculate all solute (72 POPC) SAS.
The mean total area is about 1450 A**2 with hydophilic area of 550 A**2
(supposed to be the head group). Then I will obtain only 2*SAS/(# of
lipid) = 42 A**2, which is way too small! However, I have the same value
from the pre-equilibrated POPC bilayer (64 monomers) given by Marrink.
Did I do something wrong??
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl
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