[gmx-users] Re: g_hbond output

[Jianguo Li]

A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, but 
cannot belong to both columns. 

If the program finds a pair shorter than 0.35nm, and the angle is smaller than 
30deg., then the program put this pair in the column 2.
If the program finds a pair shorter than 0.35nm, and the angle is larger than 
30deg., then the program put this pair in the column 3.

Jianguo




________________________________
From: ZHAO Lina <lnzhao99 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, 16 March 2011 15:31:30
Subject: Re: [gmx-users] Re: g_hbond output

  
 
 
 
 
 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

Here is my question, since there is already one bond formed, then why there is 
none pairs in 1000?



On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:

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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