VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 27 2006 - 17:20:57 CDT

Thanks for the reference. We'll be cleaning up the documentation. It
might be complicated adding a number of choices on Hbonding criteria (in
the user interface sense, not the programming sense), but I'll talk it
over with people here.
Peter

François-Xavier Coudert wrote:
>> 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