Re: Calculating the spin angle collective variable value

From: Giacomo Fiorin (
Date: Mon May 11 2015 - 08:40:34 CDT

Hello Marlon, without any other information about the system, the choice of
axis is up to you: ideally, the axis would represent a preferential
direction in your system, e.g. because a certain molecule is elongated in

To recalculate the value of collective variables of interest, you can now
use the "cv" command inside VMD. Version 1.9.2 has a preliminary version
of this command, the alpha version of 1.9.3 has a much better working

On Mon, May 11, 2015 at 4:51 AM, Marlon SIDORE <>

> 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

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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