From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sat Nov 22 2014 - 06:00:10 CST
Hi JC,
Can you post the config for your tilt colvar?
Jerome
On 22 November 2014 at 01:12, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> I tried your idea of replacing tilt with orientation. For an example
> frame, I get for the quaternion (0.31, 0.37, 0.59, -0.64). I then loaded
> this frame along with my reference frame, translated both so that they were
> centered on the origin, and then, using quaternion2rmatrix.tcl, applied a
> rotation. It went from something like this
>
> | /
> | /
> | /
> | /
>
> to this
>
> |
> |
> |
> | ———— (a bit misleading, it’s not perfectly aligned with any axis, but is
> certainly more planar)
>
> Clearly it doesn’t agree with the expected rotation. Comparing the
> matrices
>
> q2r
> -0.52 0.83 -0.11
> 0.04 -0.10 -0.98
> -0.84 -0.53 0.02
>
> and measure fit from VMD gives
> -0.35 -0.85 -0.39
> 0.81 -0.48 0.33
> -0.47 -0.20 0.86
>
> Shouldn’t these give the same values? What’s going on here?
>
> Thanks,
> JC
>
> On Nov 21, 2014, at 12:35 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
> Hi JC, one issue could be that the helix changes structure internally, and
> the rigid-body assumption breaks down, but perhaps you checked already for
> that.
>
> Another possibility is that the axis is not what it's supposed to be, i.e--001a113a54a4d6bac20508714e1d--
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