[gmx-users] g_hbond getting abnormal graph

minnale minnale_gnos at rediffmail.com
Thu Sep 11 09:16:52 CEST 2008


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
               
     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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