**From:** Marlon SIDORE (*marlon.sidore_at_gmail.com*)

**Date:** Mon May 11 2015 - 03:51:38 CDT

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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

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