[gmx-users] about g_hbond

Miguel Ángel Mompeán García mig.mompean at gmail.com
Fri Jan 11 13:07:50 CET 2013

Hi all,

When calculating the average number of hbonds during a simulation, does the
program g_hbond contemplate the possibility of an atom involved in two
If I visualize the structures with molden, setting the same cutoff
criterion for hbonding than g_hbond utilizes, I found out that some O atoms
are forming two H bonds with two different hydrogen atoms at once. Other O
atoms are forming just one H bond.

With g_hbond I get the same average on systems when the same O atoms are
forming two hbonds and in those where they form just one.

If the criterion is just a cutoff distance and angle, I guess I should have
seen the differences when using g_hbond with -num, but this never
happened... Any clue?

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