[gmx-users] periodic boundary condition

Itamar Kass ikass at cc.huji.ac.il
Wed Apr 30 11:20:01 CEST 2003

   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.

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
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/

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