[gmx-users] Question about g_hbond output

[Justin A. Lemkul]

Jinyao Wang wrote:
> Hi evergyone,
> 
>   I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running 
>  g_hbond -s md.tpr -f md.xtc -num numhbond.xvg
>  There are 3 columns in the output files.
> 
>   The first column = frame
>   The second column = H bonds
>   The third column = pairs within 0.35nm
>   
>   The third column value is the number of all pairs with 0.35nm including the H bonds, but why the value is less than the second column value (the number of H bonds).

Your interpretation of the column is wrong:

http://lists.gromacs.org/pipermail/gmx-users/2010-March/049505.html

-Justin

> 
> This is my output of g_hbond.
> 
> 
> @    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"
>       2000           1           0
>     2000.5           1           0
>       2001           1           0
>     2001.5           1           0
>       2002           1           0
>     2002.5           1           0
>       2003           1           1
>     2003.5           1           0
>       2004           1           0
>     2004.5           1           1
>       2005           1           0
>     2005.5           1           0
>       2006           1           0
>     2006.5           1           0
>       2007           1           1
>     2007.5           2           0
>       2008           1           0
>     2008.5           1           0
> 
> 
> 　　　　　　　 　                   Jinyao Wang
> 　　　　　　　　                    wangjy at ciac.jl.cn
> 　　　　　　　　　             　    2010-08-13
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================