From: Jianhui Tian (
Date: Thu Jul 31 2008 - 20:32:47 CDT


I used pbctools to wrap my system for better visualization. The command I
used is {pbc wrap -center "resid 1" -all}. After all is finished, I see
broken molecules, which means the whole molecule is on the edge of the new
box, half of the molecule is on one side and half on the other side and
wired bond connecting them. How can I avoid such broken molecules?

Rensselar Polytechnic Institute