[gmx-users] different g_hbond result for two run

[vivek sharma]

hi all,

I was trying to analyze some h_bond interaction for a protein with one
ligand. I tried two runs for the same one for 5 nsec and another for 10
nsec.
What I found here is that, the h-bonds present in the 5 nsec trajectory are
more than that in 10 nsec trajectory, h-bonds in 10 nsec run should be at
least equal to that in 5 nsec run.

for the two trajectory i have taken out the 10 frames. are the interaction
picked up by g_hbond are dependent on the full trajectory or the frames
only.
whether the two different run on the same input file with same parameter can
be related or compared ?

Can anybody help me in the same case by giving some explanation or giving
right way to do it ?


With Thanks,
VIVEk
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081003/9979c351/attachment.html>