[gmx-users] g_hbond

[Erik Marklund]

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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