[gmx-users] g_hbond getting abnormal graph

[Justin A. Lemkul]

minnale wrote:
> 
> Hi all,
> I have issued the command of g_hbond like this
> g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map -a 30
> while finishing of this command, it told 1 H-bond found and run 
> successfully. When I plotted .xvg file by using gnuplot its showed 
> zigzag manner graph(abnormal) and I never got this type of plot.
> for information I am sending .xvg file
> 
> @    title "Hydrogen Bonds"
> @    xaxis  label "Time"
> @    yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>         0          0          7
>       0.2          0          7     
>       0.6          0          8
>       0.8          0          7
>         1          0          8
>       1.2          0          8
>       1.4          0          8
>       1.6          0          7
>       1.8          1          8
>         2          0          8
>       2.2          0          8
>       2.4          0          7
>       2.6          1          6
>       2.8          0          9
>         3          0          8
>       3.2          0          8
>       3.4          0          6
>       3.6          0          7
>       3.8          0          7
>         4          0          8
>       4.2          0          6

Your result is perfectly fine.  The output from g_hbond reports the number of 
H-bonds per timeframe, as well as the number of contacts within the specified 
cutoff distance.

-Justin

>              
>     This 1 digit appearing often in 2 column till final time.
> 
> Could suggest me how to get proper Hydrogen bond plot.
> Thanks in advance.
>  
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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