[gmx-users] Pressure coupling for bilayer

[Itamar Kass]

itai bloch wrote:
> Hi all,
> 
> I am trying to set up a simulation of peptide in lipid bilayer with a
> file taken from Prof. Tieleman's website (dppc128.pdb). I used genbox
> for the peptide positioning (which made quite a large cavity around
> the peptide).
> I have a problem of lipids molecules that go out of the bilayer while
> doing the first position restrained run (only the peptide is fixed)
> and from what I found in the mailing list it has to do with the
> pressure coupling I use.
   Try to do some Md when the DMPC's phosphate atoms are fixed to the XY 
plane.
> I have tried both isotropic and anisotropic coupling but it seems like
> giving the same problem or just give an error due to large pressure
> oscilations and halt the run.
> Does anyone have suggestions from his own experience? I really need
> help with it.
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-- 


===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: 
http://munch.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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