[gmx-users] about g_hbond

Justin Lemkul jalemkul at vt.edu
Fri Jan 11 13:07:26 CET 2013

On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote:
> 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
> hbond?
> 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?

For O atoms with two putative H-bonds, are the donors on separate functional 
groups or molecules?  If they are not, g_hbond considers them the same, since 
that is the default behavior of the -merge option.  If you specify -nomerge, 
then the two hydrogen bonds will be considered distinct.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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