From: Hugo Azurmendi (hazur_99_at_yahoo.com)
Date: Wed Jan 11 2006 - 15:49:30 CST
Hi there,
I am running a Langevin dynamics of glucose solvated
in a periodic cell. As a result the glucose diffuse
toward the border. Other people mentioned this problem
before but I didn't find a post with an answer. I
would think that the solution would be to vary
cellOrigin with the center of mass of the molecule of
interest or some other coordinate of reference (like
C1 of glucose). If this is so, the question is how one
can get the position of an atom during a run in NAMD
to assign it to cell Origin.
Thanks,
Hugo
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