[gmx-users] periodic boundary condition

[Itamar Kass]

   Dear all, I know I will sound like I am a stupid (and maybe I am), but I did
not sure regarding the periodic boundary condition setting.  As I see it, if I
do not write something spacial in the mdp file, the system is automatically set
the boundary.  But when I run gromacs on my system, some atoms are out of the
simulation box.
   I wanted to now, first theoretically, if the boundary are properly set how
can it be?  As I understand it, if an atom x moves through a wall into box y
(from the simulation box), the same x atom, from the opposite box (to the y box)
should enter the simulation box.  Hence the amount and composition of atoms in
the simulation box should remain the same.
   Second, if I should set the periodic boundary condition how this is handle in
the mdp file?  Is there any tutorial regarding it?

         Thank in advance, Kass.


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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
| Email: ikass at cc.huji.ac.il
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/
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