[gmx-users] Re: g_hbond output

[Jianguo Li]

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 <lnzhao99 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at 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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