[gmx-users] water mediated Hbond

[Bratin Kumar Das]

Hi
    In md analysis you can calculate continuous h-bond. That will give you
proper lifetime.

On Tue 14 May, 2019, 11:58 AM Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
wrote:

> In gromacs you can not calculate h-bond life time. You can use mdanalysis
> tool for calculating h-bond lifetime.
>
> On Tue 14 May, 2019, 11:56 AM , <spss4 at iacs.res.in> wrote:
>
>>   Then what is the right way to calculate lifetime of a hydrogen bond?
>> ----- Message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
>> ---------
>>     Date: Mon, 13 May 2019 22:24:51 +0530
>>     From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
>> Reply-To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] water mediated Hbond
>>       To: gmx-users at gromacs.org
>>
>> > The lifetime of the h-bond can be calculated by calculating the
>> > autocorrelation of continuous h-bonds. I don't think gmx h-bond is
>> suitable
>> > for continuous hydrogen ACF. It can give the intermittent h-bond ACF
>> which
>> > can be helpful for calculating the structural relaxation.
>> >
>> > On Mon 13 May, 2019, 8:51 PM , <spss4 at iacs.res.in> wrote:
>> >
>> >> Hii
>> >> Thank you for your reply. So as u suggest I have to calculate 2 Hbond
>> >> separately. But for how long that water mediated Hbond is stable; for
>> >> that can I use Hbond number with time? For how many frames both the
>> >> bonds appearing together. Is this right? One more thing is that I want
>> >> to calculate lifetime of the Hbond. I have used gmx hbond -ac -contact
>> >> command. Then I am getting a time dependent autocorrelation function.
>> >> Integration of the C(t) will give me lifetime of the Hbond. Is this a
>> >> right way to proceed?
>> >>
>> >> ----- Message from Justin Lemkul <jalemkul at vt.edu> ---------
>> >>     Date: Mon, 13 May 2019 09:10:41 -0400
>> >>     From: Justin Lemkul <jalemkul at vt.edu>
>> >> Reply-To: gmx-users at gromacs.org
>> >> Subject: Re: [gmx-users] water mediated Hbond
>> >>       To: gmx-users at gromacs.org
>> >>
>> >> On 5/13/19 8:48 AM, Bratin Kumar Das wrote:
>> >> Hi,
>> >>       You can make a ndx file containing the residue of interest and
>> the
>> >> SOL. In gmx h-bond command use the index file. It will give you water
>> >> mediated hbond
>> >>
>> >> That's not what a water-mediated hydrogen bond is. That's when a
>> >> water molecule simultaneously participates in hydrogen bonds with
>> >> two other species. GROMACS does not have the ability to do such
>> >> calculations easily. It would require one calculation of H-bonds
>> >> between species A and water, saving those waters into index groups
>> >> per frame, and then computing the H-bonds of those waters with
>> >> species B in a separate calculation. Only then do you get the number
>> >> of water-mediated (not direct) hydrogen bonds.
>> >>
>> >> -Justin
>> >>
>> >> On Tue 7 May, 2019, 12:40 PM , <spss4 at iacs.res.in> wrote:
>> >>
>> >> Dear all
>> >> I want to determine the water mediated hydrogen between DNA bases and
>> >> small molecule. What extra flag should I use in gmx hbond command? Is
>> >> there any other option to capture the water mediated Hbonds? Please
>> >> suggest something.
>> >> Sunipa Sarkar
>> >> --
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>> >> --
>> >> ==================================================
>> >>
>> >> Justin A. Lemkul, Ph.D.
>> >> Assistant Professor
>> >> Office: 301 Fralin Hall
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>> >>
>> >> Virginia Tech Department of Biochemistry
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>> >>
>> >> jalemkul at vt.edu | (540) 231-3129
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>> >>
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>> ----- End message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
>> -----
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