[gmx-users] Question about g_hbond output

[Jinyao Wang]

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).

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