[gmx-users] press coupling

[xu yechun]

Dear all,
    I think maybe the simulation of membrane is more difficult than systems 
in water. I have insterted one helix into 127 popc lipids which was 
downloaded from Dr. Peter Tieleman's homepage. However, the deformation of 
the system(lipid+water+helix) is big whether I used NPT or NVT method with 
different parameters from mail list and references. The system changed from 
a cuboid into a cylinder, water penetrated into the hydrophobic region of 
lipids, and the tails of boundary lipids tilted from the z axis. I could 
not find a set of proper parameters to keep the system in origin 
formation(cuboid). All the pdb files from Dr. Peter Tieleman's homepage are 
cuboid, but how can I keep that in my simulation? Any information is 
appreciated. Especially, I hope that someone who have successfully 
simulated the bilayer lipids will show his *.mdp file on this mail list.

Thanks in advance

Xu yechun

Shanghai Institute of Meteria Medica,
Shanghai Institutes of Biological Sciences,
Chinese Academy of Sciences, 
294 Taiyuan Road, Shanghai 200031,
P. R. China

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