[gmx-users] g_hbond

Carla Jamous carlajamous at gmail.com
Tue Nov 2 17:35:58 CET 2010

Hi to all,

I'm sorry I'm asking again a question I asked a week ago but I still haven't
found my answer:

I concatenated 3 trajectories of 3 different molecules (that have the same
number of atoms) with trjcat: trjcat -settime

Then I ran g_hbond on the concatenated trajectory, I got an index.ndx file
that contains an H-bond between the Thr121 of my protein and an atom N2 of
my ligand. This H_bond  figures in the 3 trajectories when I look at the
hbmap of my concatenated trajectory.

On the other hand, I ran g_hbond on each of the 3 different trajectories.
This H_bond doesn't exist in the index files of two of my trajectories. So
it doesn't match the result I get with my concatenated trajectory.

To be sure that this result is right, I calculated the angle and the r of my
H-bond in VMD during each of the 3 trajectories and the results indicate
that this H-bond doesn't exist (I consider that r must be < or equal to 0.35
nm and angle < or equal to 30 degrees).

Please can anyone tell me why the results of g_hbond in my concatenated
trajectory don't match the results of g_hbond on each of my trajectories?

Thank you

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