[gmx-users] water mediated Hbond

[Bratin Kumar Das]

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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> >>
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> ----- End message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> -----
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