[gmx-users] g_hbond

[Nilesh Dhumal]

I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between
hydrogen and O,acceptor) using g_hbond,

g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc
-r 0.25 -contact -dist

The found the calculated number of hydrogen bond along time are zero and
-nan is the in hbdist.xvg file.
I calculated the distance between hydrogen and oxygen using g_dist and the
calculated the distance is less than 0.25 nm.

Why am I getting zero number of hydrogen bonds using g_hbond (based on
same cutoff )?

Nilesh



> Thanks.
>
> I will use two groups.
>
> Nilesh
>>
>> On 7/9/15 9:13 PM, Nilesh Dhumal wrote:
>>>>
>>>>
>>>> On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
>>>>> Hello,
>>>>>
>>>>> I am calculating g_hbond for water system.  I have a question about
>>>>> specifying two group for calculating hydrogen bond.
>>>>>
>>>>> Do I specify atoms in triplet(O-H---O)?
>>>>> Can I specify O-H as one group (Donor-Hydrogen) and O in other group
>>>>> (Acceptor)?
>>>>
>>>> If the system is pure water, you do not need any special index groups.
>>>
>>> I have DMSO in the system. I just mentioned water to make it simple.
>>> I am interested in O--H---O(DMSO) interactions?
>>>
>>> How should I specify this?
>>>
>>> With one triplet O--H---O(DMSO) or two groups one O--H and second
>>> O(DMSO)
>>
>> The latter - just use DMSO and water groups.  O can be a donor or
>> acceptor, and
>> g_hbond intelligently figures out whether or not a given atom is a donor
>> or
>> acceptor (or both).
>>
>> -Justin
>>
>>>>
>>>>> Default  -r cutoff is 0.35nm. Is the distance between
>>>>> hydrogen---acceptor
>>>>> or distance between donor---acceptor?
>>>>
>>>> Read the first sentence of the help description.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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>
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