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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> >>
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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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