[gmx-users] Membrane box during simulation

Itamar Kass ikass at cc.huji.ac.il
Wed Dec 17 21:37:01 CET 2003

  Hi, I have a technical question regarding simulation box.  In my simulation I
use a box there are DMPC bilayer with a channel and water with ions.  
  The starting positions were perfectly shaped, mean that when viewed using VMD
the shape of a box was shown.  PR dynamics gives a disastrous results, the box
like shape of the system was lost.
  At first I thought it was a results of using isotropic pressure coupling, but
changing to semiisotropic (where the membrane can not expand nor shrink):

Pcoupl              =  berendsen
pcoupltype          =  semiisotropic
tau_p               =  1 1
compressibility     =  0 4.5e-5
ref_p               =  1.0 1.0

gives the same results. 
  My guess is that the issue concerned the periodic boundary condition. Does
anyone has any idea regarding the problem, and how to solve it? 

         Thanks, Itamar.

p.s. the simulation box is produced as "editconf -f system.pdb -o system_box.pdb
-box 6.1059 6.1059 6.5853 -angles 90 90 90 -c

Computers are like airconditioners... They don't work well with Windows

| 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://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html

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