**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Mon May 11 2015 - 08:40:34 CDT

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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

shape.

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

version.

On Mon, May 11, 2015 at 4:51 AM, Marlon SIDORE <marlon.sidore_at_gmail.com>

wrote:

*> Dear all,
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*>
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*> I have been trying to recalculate (using my own scripts) the value of the
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*> spin angle along a trajectory for trajectories where the collective
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*> variable was not set. As the collective variable is only a subset of the
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*> orientation colvar, I tried to calculate it.
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*>
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*> I could use the 2004 paper (Using quaternions to calculate RMSD) to obtain
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*> the particular quaternion (which corresponds to the sought rotation) ...
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*> However I have been stuck for a while at this step, probably due to a lack
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*> of maths training.
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*>
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*> The colvars manual says that this rotation corresponds to two rotations, a
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*> rotation around an axis and a tilt rotation around an axis orthogonal to
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*> the previous axis. The rotation I need (the spin angle) is the first one.
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*>
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*> It seems that I need to know the axis beforehand: how ? And once I have
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*> it, there's a formula to get the rotation given this axis, but do I need to
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*> do something more to differentiate the rotation from the tilt ?
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*>
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*> Thanks for your attention, and sorry if it all comes down to my lack of
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*> math training.
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*> Best regards,
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*>
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*> Marlon Sidore
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*>
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-- 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 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/

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