Re: tilt colvar

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 21 2014 - 18:12:31 CST

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, its not perfectly aligned with any axis, but is certainly more planar)

Clearly it doesnt 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

Shouldnt these give the same values? Whats 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. 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 dont 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 its 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, its 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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