From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Feb 06 2012 - 16:55:26 CST
To answer part of my own question
> Is the colvars module using the same algorithm for molecule alignment as
The colvar module uses quaternations for finding the optimal rotation. So I
can define an orientation colvar and a DistanceVec colvar to obtain the
full transformation matrix, which would enable me to visualise exactly what
is going on using VMD.
By the way, where can the script " quaternion2rmatrix.tcl" be found?
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