From: JAVAD NOROOZI (noroozijavad_at_yahoo.com)
Date: Mon Jan 19 2015 - 23:55:19 CST
As far as i know NAMD does not wrap atomic coordinates to the other side of the box until the center of mass of the molecule composed of those atoms pass the boundary.
The question is what would happen if one specify the periodic box dimension much smaller than the max-min of the initial coordinate file(#.coord)?
In this case center of mass of some molecules stick out the box, does NAMD wrap them to the other side in the very first step?
What if some atoms in a molecule stick out (not the molecule center of mass ) of box?
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