[gmx-users] separating bilayer leaflets - POPC vs. DMPC and DPPC

David L. Bostick dbostick at physics.unc.edu
Sat Sep 10 04:35:04 CEST 2005

Hi Rama,

Yes, that's what I mean.  if you can constrain the area by setting the xy
compressibility to 0, you have effectively what is called an NPnAT
ensemble, where "Pn" is the component of pressure normal to the bilayer
interface. It should give a similar result to NVT, but with the advantage
that density in the z-dimension is allowed to equilibrate as well.  Then
once things converge well enough, switch ... just as you said.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Fri, 9 Sep 2005, Ramachandra Rao Gullapalli wrote:

> If you can prescribe an area and run the bilayer for some time (1-2 ns) in a
> constant area, constant pressure ensemble, and then switch to semiisotropic
> pressure coupling, this could fix it.
> Dear Dr Bostick,
> I quite don t understand what you mean by a constant area,constant pressure
> ensemble. Do you mean you assign parameters of 0.0 and 4.5e-5 compressibility
> in xy and z respectively under semiisotropic coupling for constant area and
> constant pressure?
> And then you shift to 4.5e-5 and 4.5e-5 compressibility in xy and z respectively
> for a "proper" semiisotropic coupling?
> I was confused regarding this point when you had replied to my earlier question
> last month.
> Thank you for your time
> Regards
> Rama
> The important thing is not to stop questioning. Curiosity has its own reason for existing...
> -Einstein
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