Re: Colvars Orientation Question

From: Xander Gonzalez (
Date: Fri Jul 05 2019 - 14:22:34 CDT

Thank you for the response. I have checked the colvars.traj file and the
beginning quaternions are significantly different than the center colvars
set in the configuration file, and the final quaternions are different than
the target centers. I also visualized the rotations with the script you
sent, it seems like the initial rotation is caused by the second collective
variable rotating about 90 degrees. I have tried setting the target center
for the second colvar quaternion to be the same as it's center to see if
this would keep this rotation from happening, but I get the same result.


On Wed, Jul 3, 2019 at 3:54 AM Jérôme Hénin <> wrote:

> 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--000000000000e48657058cf404c0--

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