[gmx-users] pressure coupling for lipid bilayer
periole at inka.mssm.edu
Thu May 2 03:08:39 CEST 2002
Shang-Te Danny Hsu wrote:
> 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 ....
> 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.
> Surface tension coupling method is suggested to be a nice approach (J.
> Chem. Phys. 111(3):1281), but the parameters are not trivial. Without
> experimental data on hand, it is difficult to estimate surface tension
> (in my case, POPC bilayer). In addition, the incorporation of other
> molecules may alter the surface tension again!
> How should I setup up such a system properly???
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
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
Dept. of Physiology and Biophysics
Mount Sinai School of Medicine-NYU
New York, NY 10029
More information about the gromacs.org_gmx-users