[gmx-users] g_hbond output

[vedat durmaz]

hi out there,

still doing my first steps on the gmx planet. can anyone tell me, why
there are 3 columns in the output file of g_hbond and how to interpret
the output values when having run

g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg

first column frame!
second column = #H bonds?
third column = #all pairs within 0.35nm?? which pairs?? including all H
bonds??? if yes, how can this value be less than the respective #H bonds
for some frames? (see output below).

i have counted the number of H bonds with "vmd" additionally (same angle
and distance cut off), but they do not correlate with the ones here ...

what am i doing wrong?

output gmx:
@    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           2           3
      0.02           2           3
      0.04           2           3
      0.06           2           1
      0.08           2           1
       0.1           2           1