[gmx-users] g_hbond getting abnormal graph

[minnale]

Thanks Justin for your response
you are telling that whatever generated output .xvg files of two systems from g_hbond is perfect. But when I plot .xvg files with help of "xmgrace" it depicting hydrogen bonds represents at bottom and contact pairs above in one plot(one system).I am sending file in .xvg format. Could you open in xmgrace and suggest me whether what I have done is correct or not.
Thanks in advance.

>On Thu, 11 Sep 2008 Justin A.Lemkul wrote :
> >
> >
> >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.
> >>
> >>
> >>
> >>Rediff Shopping <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2206641_2199021/2201649/1?PARTNER=3&OAS_QUERY=null>
> >>
> >>
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> >>
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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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