[gmx-users] about g_hbond

Miguel Ángel Mompeán García mig.mompean at gmail.com
Fri Jan 11 19:10:21 CET 2013

The donors are two H atoms from the amide group of Gln residues. Thus,
I will try the -merge option. Thank for the comment.

I wonder if the following issue is affecting gromacs 4.5.5:


2013/1/11, Justin Lemkul <jalemkul at vt.edu>:
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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