VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Sep 26 2006 - 12:24:46 CDT

Hi François,
the documentation's wording probably ought to be tweaked -- a better
description would be
"Given an atom D with a hydrogen H bonded to it and an atom
     A not bonded to atom D"

The angle criterion is indeed D-H-A -- this is the relevant angle for
hbond energies as well, as you're testing for collinearity of the donor,
hydrogen, and acceptor in that order. In your case, the D-H-A angle is
42.39 degrees, which is where the hydrogen bond begins to show up.
Does this make sense?
Best,
Peter

François-Xavier Coudert wrote:
> Hi all,
>
> I have a problem understanding the criterion used for HBonds
> representation. From the doc:
>
> Given an atom D with a hydrogen H bonded to it and an atom
> A with no hydrogen bonded to it, a hydrogen bond exists between
> A and H iff the distance ||D-A|| < dist and the angle D-H-A < ang,
> where ang and dist are user defined.
>
> I assume the angle criterion is H-D-A < ang rather than D-H-A, and I
> don't think the "atom A with no hydrogen bonded to it" is enforced,
> otherwise no H bond would ever occur in water. Nonetheless, in the
> attached xyz file, the DA distance is 2.59 (as labeled by VMD itself)
> and the HDA angle is 27.98 (once again measured by VMD). But in Hbonds
> representation with distance cutoff 3.5 and angle cutoff 30, no H bond
> is displayed (I use VMD 1.8.5).
>
> I supposed there's something I've overlooked, but what?
>
> Thanks for your help,
> FXC