Colvar orientation and CoG

From: Nicolas Martin (
Date: Thu Jun 16 2016 - 09:02:28 CDT

Dear users,

I am currently trying to restrain a complex motion in a protein. I have
a starting and an end structure that I use to compute a quaternion with
NAMD. The rotation I get is described by an angle inferior to 90 deg and
for which the center is not the center of geometry of my selection. You
can see the motion I'm trying to describe more as an hinge motion than a
self rotation.

In a second time I tried to use this quaternion and a harmonic restrain
on my starting structure to reproduce the end structure. Since the axis
of the rotation described by the quaternion previously computed is
translated toward the cog of my selection (I think I saw that into the
source code of spinangle and orientation) the rotation applied is
different from the one I initially computed since the axis / center of
rotation are different.

So here are my two questions. Can one just comment the lines
corresponding to the translation in the code ? And if no why?

Thanks a lot for the advice, bests


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