[gmx-users] RE: Bonds and atom-pairs in g_hbond
adeyoung at andrew.cmu.edu
Mon Jun 11 23:41:44 CEST 2012
I just realized that the output from g_hbond using the -num flag (by
default, the file name is hbnum.xvg) also seems to make a distinction
between "hydrogen bonds" and "pairs within the distance." For example, here
are the first few lines of this output file:
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.227905 nm"
0 39 1
0.05 40 2
0.1 40 2
0.15 40 1
0.2 41 0
0.25 38 3
0.3 39 2
where 0.227905 nm is the value that I give to -r. Why are there so many
more "hydrogen bonds" than "pairs within -r", if the latter seems to be a
necessary but not sufficient condition for the former?
Carnegie Mellon University
From: Andrew DeYoung
Sent: Monday, June 11, 2012 5:31 PM
To: gmx-users at gromacs.org
Subject: Bonds and atom-pairs in g_hbond
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
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!
Carnegie Mellon University
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