[gmx-users] Bonds and atom-pairs in g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Tue Jun 12 09:15:06 CEST 2012


The second set is pairs that are within h-bonding distance but that fails to fulfill the angular criteriion. The text output is hence somewhat misleading.


11 jun 2012 kl. 23.30 skrev Andrew DeYoung:

> Hi, 
> I am analyzing hydrogen bonds using g_hbond.  I have selected two
> non-overlapping groups; one is hydroxyl groups (OH, where O is the donor and
> H is the hydrogen), and the other is oxygens on PO4^3- (where F is the
> acceptor).  I am using the switch -noda, which tells the program to take the
> -r value as the Hydrogen-Acceptor distance (here, H-O), rather than the
> Donor-Acceptor distance (here, O-O).  My trajectory is 10 ns long.
> In the output after the calculation, I see the following:
> Found 233 different hydrogen bonds in trajectory
> Found 224 different atom-pairs within hydrogen bonding distance
> Can you please help me to understand the terms "hydrogen bond" and
> "atom-pair within hydrogen bonding distance" conceptually?
> I think that in order for a hydrogen and an acceptor to be considered
> hydrogen bonded, two criteria must be satisfied: (1) the distance (in this
> case, the distance between the hydrogen and the acceptor, since I am using
> -noda) must be less than the cutoff distance -r, and (2) the
> Acceptor-Donor-Hydrogen angle must be less than the cutoff angle -a.  So
> distance and angle are the two criteria that must be met, according to
> g_hbond and most definitions of hydrogen bonding.
> So, apparently, g_hbond found 233 hydrogen bonds satisfying both the
> distance and angle criteria.
> But, g_hbond "found 224 different atom-pairs within hydrogen bonding
> distance."  My guess is that this means that there are 224 atom pairs
> satisfying the distance criterion (i.e., Hydrogen-Acceptor pairs within the
> cutoff distance, -r).  But if my interpretation of the term "atom-pair
> within hydrogen bonding distance" is correct, how can there be 9 _fewer_
> atom pairs that satisfy only the distance criterion (and not the angle
> criterion), than those that satisfy _both_ the distance criterion _and_ the
> angle criterion?
> Probably, I have the wrong pictures of the terms "hydrogen bond" and
> "atom-pair within hydrogen bonding distance" in my head.
> Thank you for your time!
> Andrew DeYoung
> Carnegie Mellon University
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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