[gmx-users] g_hbond

Erik Marklund erik.marklund at chem.ox.ac.uk
Sat Jul 11 12:23:37 CEST 2015 

Hi Nilesh,

You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg.

Kind regards,
Erik

> On 10 Jul 2015, at 15:58, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
> 
> I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?
> 
> Nilesh
> 
>> But without contact you will need a full donor-hydrogen-acceptor triad for
>> it to be registered, which is not what you want as far as I can tell.
>> 
>> Erik
>> 
>>> On 10 Jul 2015, at 15:17, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
>>> 
>>> This is index file
>>> 
>>> [ O8-H18-1 ]
>>>  8  18
>>> [ O8-H18-2 ]
>>> 4032
>>> 
>>> 
>>> Found 1 donors and 2 acceptors
>>> 
>>> Its look contact YES check the distance between accetpr---donor.
>>> 
>>> I will run without contact.
>>> 
>>> Nilesh
>>> 
>>>> Hi Nilesh,
>>>> 
>>>> Am not sure it accepts hydrogens as donors/acceptors even with
>>>> -contact.
>>>> How many donors and acceptors are found?
>>>> 
>>>> Kind regards,
>>>> Erik
>>>> 
>>>>> On 10 Jul 2015, at 14:37, Nilesh Dhumal <ndhumal at andrew.cmu.edu>
>>>>> wrote:
>>>>> 
>>>>> 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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