[gmx-users] Membrane box during simulation

[Tsjerk Wassenaar]

Hi Itamar,

I would say you're right about the effect you're seeing coming from PBC, 
but I wouldn't call it a problem. Your simulation system is infinite, so 
molecules can drift. You can put them back with

trjconv -s topol.tpr -f traj.xtc -o trajout.xtc -pbc inbox

Groetnis,

Tsjerk

Itamar Kass wrote:

>  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
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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
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