If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff
distance and the cutoff angle. $3 is the number of pairs within the cutoff
distance, but beyond the cutoff angle. You may got different number of hbonds
using different cutoff distance and cutoff angle.
Jianguo
________________________________
From: ZHAO Lina <lnzha...@gmail.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Wednesday, 16 March 2011 13:33:57
Subject: [gmx-users] Re: g_hbond output
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
0 0 0
200 0 0
400 2 1
600 0 3
800 0 2
1000 1 0
:
50000 3 2
Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the
$3
means pairs.
I tried pymol, and on the last frame,
there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2
Thanks and sorry for last email without my realization it sent.
lina
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