target molecular moves away from water box

From: laura (
Date: Sun Oct 22 2006 - 20:18:11 CDT

              I have runned my molecular in period water box for a long time
, about 2ns, target molecular moved out of water box. I counted the
number of hydrogen bonds between target molecular and solution from the
dcd file, the number was zero when the target molecular moved out of water
box. I don't know what it means and whether it will make the results
totally nonsense. If I want to fix my target molecular but not water, how
I write script ? The command COMmotion maybe act on entire system.

             I ever seen some VMD users said " the command measure hbonds
is not aware of PBC, and will miss whatever bonds may extend across the
edges of the period box ", how I to translate a part of the system by a
periodic repeat distance?

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