[gmx-users] about g_hbond
jalemkul at vt.edu
Fri Jan 11 19:15:31 CET 2013
On 1/11/13 1:10 PM, Miguel Ángel Mompeán García wrote:
> 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:
No, that issue was fixed before the 4.5.5 release.
> 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
>>> 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
>>> are forming two H bonds with two different hydrogen atoms at once. Other
>>> 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
>>> 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,
>> 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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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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