[gmx-users] g_hbond and contact

[Kavyashree M]

Dear users,

I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
>From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.
The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?
Also the xvg file looks like -

s0 legend "Contacts"
@ s1 legend "Pairs within 0.4 nm"
      4000        7496           0
      4002        7513           0
      4004        7605           0
      4006        7531           0
      4008        7573           0
      4010        7546           0
      4012        7544           0
      4014        7526           0
      4016        7530           0
      4018        7496           0
      4020        7526           0
..


Thank you
kavya