[gmx-users] g_hbond

[Nilesh Dhumal]

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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