[gmx-users] lipid gel phase simulation model building

[Carsten Selle]

Dear gromacs users,

the gel phase of some lipids as the L beta prime of DPPC is 
characterized by all-trans alkyl chains which are tilted with respect to 
the bilayer normal. I would like to set set up a system analog to the 
one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000), 
pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).  
I tried editconf and genbox to  generate a cubic simulation box and a 
suitable aqueous environment for the bilayer I generated from crystal 
data. However, since the box is cubic, there is plenty of room for 
unwanted water-alkyl interaction. genbox accordingly placed water in 
hydrophobic places.  The water molecules should (almost) only interact 
with with the lipid headgroups and water. Any helpful comment is greatly 
appreciated.

Best regards,
Carsten

-- 

Dr. Carsten Selle
University of Leipzig
Institute for Experimental Physics I
PWM
Linnestr. 5
D-04103 Leipzig
Germany