[gmx-users] water mediated Hbond

[Bratin Kumar Das]

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.
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