[gmx-users] Pressure coupling for bilayer

[itai bloch]

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.
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.