From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 21 2014 - 11:09:55 CST
I think I still donít 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 itís 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, ďtiltĒ is around +/- 0.02. But when I look at the frames by eye, itís clearly not the case. What I see is this (R is ref and C is current):
when what I expect is this
| _ _ _ _ _ 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?
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