VMD-L Mailing List

From: François-Xavier Coudert (fxcoudert_at_gmail.com)
Date: Wed Sep 27 2006 - 03:17:01 CDT

> I do mean the angle between vectors HD and HA, \hat{DHA}. You might want
> to measure this again, because in your original email you said that the
> angle you were expecting was 27.98, which is the angle between vectors
> HD and DA, and is not related to the quantity of interest (this was
> measured in VMD).

Doh, I think I got it. For me, \hat{DHA} = 137.6 degrees, because it's
then angle between vectors HD and HA, which is
acos(dot_product(HD,HA)/(norm(HD)*norm(HA))). And if D, H and A are
aligned, then \hat{DHA} = 180 degrees, which is okay.

But your 42.4 angle is the complement to 180 degrees, which is angle
between vectors DH and HA.

Well, anyway, I think it's clear now. I'd suggest rewording the
documentation so that no confusion is possible. I'll work on a tlc
script for my own use, but would be glad to help VMD provide a few
different choices for HBonds criteria (the one I usually use is from
A. Luzar, D. Chandler, Nature 1996, 379, 55­57).

Thanks again,
FX