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

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

**Next message:**Marlon SIDORE: "Re: Calculating the spin angle collective variable value"**Previous message:**Marlon SIDORE: "Calculating the spin angle collective variable value"**In reply to:**Marlon SIDORE: "Calculating the spin angle collective variable value"**Next in thread:**Marlon SIDORE: "Re: Calculating the spin angle collective variable value"**Reply:**Marlon SIDORE: "Re: Calculating the spin angle collective variable value"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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,
*

*>
*

*> 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 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/

**Next message:**Marlon SIDORE: "Re: Calculating the spin angle collective variable value"**Previous message:**Marlon SIDORE: "Calculating the spin angle collective variable value"**In reply to:**Marlon SIDORE: "Calculating the spin angle collective variable value"**Next in thread:**Marlon SIDORE: "Re: Calculating the spin angle collective variable value"**Reply:**Marlon SIDORE: "Re: Calculating the spin angle collective variable value"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Thu Dec 31 2015 - 23:21:52 CST
*