[gmx-users] Re: g_hbond output

[ZHAO Lina]

 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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