Re: Colvars Orientation Question

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Jul 03 2019 - 03:53:44 CDT

One last point: quaternions values are not very intuitive. If it helps, you
can visualize them as a rotation axis and lines indicating the value of the
angle. Load a trajectory in VMD, source this script and use the
"start_rotation_display" command, with the name of the orientation colvar.
https://github.com/Colvars/colvars/blob/master/vmd/scripts/colvar_display.tcl

Best,
Jerome

On Wed, 3 Jul 2019 at 10:49, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Alexander,
>
> the explanation to this mystery might be in the colvars.traj file. Look in
> particular for the initial and final values of the orientation quaternion--0000000000009a60e2058cc3007c--

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