[gmx-users] g_hbond

Carla Jamous carlajamous at gmail.com
Tue Nov 9 15:08:15 CET 2010

Hi everyone,

I ran g_hbond on a trajectory. When g_hbond asks for two groups in the index
file, I give:
group1: "Protein"
group2: "ligand"
The output .ndx file contains 44 Hbonds.

In order to verify my result on each and every Hbond, I ran g_hbond on the
same trajectory but this time in my index file, I gave atom triplets, so
when g_hbond asks for two groups, I give for example:
group1: "a4810_a4811_a1857"
group2: "a4810_a4811_a1857"
Surprisingly, 10 of the 44 Hbonds are not found using this method.

Am I doing something wrong or is there a problem with g_hbond?

Thank you,

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