[gmx-users] water mediated Hbond

Fri May 17 10:03:46 CEST 2019

Hi,
    There are two types of hydrogen bond from dynamic point of view. 1)
intermittent and 2) continuous. Between two type of hydrogen bond
continuous h-bond autocorrelation will give you proper lifetime ...not
intermittent. In gmx h-bond if we give the ACF of intermittent h-bond.
Therefore it's better to go for md-analysis..there you find code for
continuous h-bond ACF which you give proper h-bond life time in which area
you want to calculate.

On Fri 17 May, 2019, 11:00 AM , <spss4 at iacs.res.in> wrote:

>   Hi
> In gmx hbond command there is a flag -ac -contact which gives hbond
> autocorrelation function with respect to time. Can I use that to get
> idea about lifetime of a Hbond? Because integration of the
> autocorrelation function will give the lifetime. Is there anything
> wrong?
>
> ----- Message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> ---------
>     Date: Tue, 14 May 2019 19:21:19 +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
>
> > 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
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> >>> ----- End message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
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> ----- End message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> -----
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