Calculating the spin angle collective variable value

From: Marlon SIDORE (
Date: Mon May 11 2015 - 03:51:38 CDT

Dear all,

I have been trying to recalculate (using my own scripts) the value of the
spin angle along a trajectory for trajectories where the collective
variable was not set. As the collective variable is only a subset of the
orientation colvar, I tried to calculate it.

I could use the 2004 paper (Using quaternions to calculate RMSD) to obtain
the particular quaternion (which corresponds to the sought rotation) ...
However I have been stuck for a while at this step, probably due to a lack
of maths training.

The colvars manual says that this rotation corresponds to two rotations, a
rotation around an axis and a tilt rotation around an axis orthogonal to
the previous axis. The rotation I need (the spin angle) is the first one.

It seems that I need to know the axis beforehand: how ? And once I have it,
there's a formula to get the rotation given this axis, but do I need to do
something more to differentiate the rotation from the tilt ?

Thanks for your attention, and sorry if it all comes down to my lack of
math training.
Best regards,

Marlon Sidore

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:07 CST