Subject: periodic boundary condition in CHARMM

From: Niharendu.Choudhury-.at.-mail.uh.edu
Date: Thu, 26 Jun 2003 15:45:49 -0500 (CDT)

Hi ccl-users
I am a new CHARMM user.
In CHARMM (version c26b1) for liquid water simulation  with PERIODIC BOUNDARY CONDITION in a cubic box with box length say 31.063 angstorm, if i use the following command is that okay. 
command i used:

Crystal Define Cubic  31.063 31.063  90.0 90.0 90.0
Crystal Build noperations 0

Do the above  commads mean coordinates of all the particles, those are out of the primary box, in EVERY dynamic TIME STEP will be set back in the primary simulation box?

If so, then in my final output coordinate file, I found some coordinates which are outside the box, say -20.5 and 20.05 etc. 

Please explain.
Nihar