[gmx-users] g_hbond output

[David van der Spoel]

On 2010-03-17 16.26, vedat durmaz wrote:
> 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).
Pairs that are not hbonded due to wrong angle.

>
> 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?
Definition (angle, cutoff) may be different.
>
> 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


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