Re: Orientation Colvars Question

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Aug 12 2019 - 05:45:23 CDT

Hi Alexander,

you could try the Colvars Dashboard plugin of VMD (just appeared in recent
alpha releases) to troubleshoot this. That's a new tool, so please let me
know how it goes.

Best,
Jerome

On Tue, 30 Jul 2019 at 00:22, Xander Gonzalez <xandergonz1_at_gmail.com> wrote:

> Hello,
>
> I have been following the "Exploring Complex Conformational Transition
> Pathways" tutorial and trying to apply it to my own structure. In my case I
> am trying to rotate two segments of a structure away from each other, using
> one colvar for each segment. When I use the orientation.tcl script modified
> with the correct atom selections I get seemingly incorrect quaternions, in
> the trajectories the protein first distorts slightly and then does not move
> further. I would really appreciate any troubleshooting ideas about this.
> Thank you for your time.
>
> Regards,
> Alexander
>

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