[gmx-users] g_hbond on trajectory

[Jennifer Vo]

Dear All,
I used g_hbond to analyze the possible hydrogen bonds between protein and
solvent (water) over the trajectory with this command:
g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g
hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg

The log file showed me:
....
  SER141OG      SER141HG     SOL2920OW
  SER141OG      SER141HG     SOL4449OW
  SER141OG      SER141HG     SOL5073OW
  SER141OG      SER141HG     SOL11886OW
  SER141OG      SER141HG     SOL13715OW
....
I wonder if this calculation is based on one coordinate file (if yes, which
one!?) or the average structure over trajectory?
Many thanks in advance.
Regards,
Jennifer