[gmx-users] about g_hbond

[Justin Lemkul]

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:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
>

No, that issue was fixed before the 4.5.5 release.

-Justin

> 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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-- 
========================================

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

========================================