center-of-mass tcl and coordinate wrapping

From: Ilja Khavrutskii (
Date: Sun Feb 24 2008 - 15:45:15 CST


I have written a tcl script to restrain centers of mass of several groups
of atoms and noticed that NAMD appears to have somewhat interesting
coordinate wrapping procedure. If an atom from any of the center-of-mass
groups crosses the periodic boundary, its positions in the tcl forces
script do not change abruptly as I expected (which I thought was very
nice), but when I restart a simulation where such an atom or several of
them have been wrapped, it usually crashes upon restart because the
coordinates of the wrapped atoms have been reset to reside within the
primary box and hence all the history available in tcl has been lost.

I was just curious if there was a way to restart/propagate a simulation in
a way where the center of mass positions will be continous. Would
appreciate if anybody could comment on this or correct me if I got it


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