From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Nov 21 2014 - 11:35:25 CST
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.
it is not the z-axis?
If it helps, this is the function that calculates the tilt component:
https://github.com/colvars/colvars/blob/master/src/colvartypes.h#L1487
And if you replace the "tilt" component with an "orientation" component,
which is defined without the preferential axis, you can get the full
quaternion (q0, q1, q2, q3). With it, it should be possible to see whether
the problem is the orientation, or the preferential axis.
Giacomo
On Fri, Nov 21, 2014 at 12:09 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> I think I still don’t understand this correctly. I have the case of a
> small helix with its reference state being parallel to the membrane (z)
> axis. I then want to sample a state where it’s parallel to the surface
> instead, meaning the tilt angle should be 90 deg. and cos(theta) = 0.
> Colvars tells me this is the case - for the frames of a given trajectory,
> “tilt” is around +/- 0.02. But when I look at the frames by eye, it’s
> clearly not the case. What I see is this (R is ref and C is current):
>
> R C
> | /
> | /
> | /
> | /
>
> when what I expect is this
>
> R
> |
> |
> |
> | _ _ _ _ _ C
>
> (I hope my ascii art comes through correctly).
>
> When I calculate the angle for the case I actually observe, I get about 25
> deg. What am I missing here?
>
> Thanks!
> JC
>
>
-- 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/
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