[gmx-users] g_hbond getting abnormal graph

[David van der Spoel]

minnale wrote:
> 
> 
> 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.
Justin already answered your question.
Please don't put the same question twice.

> 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 
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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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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se