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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