[gmx-users] water mediated Hbond

[spss4 at iacs.res.in]

  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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----- End message from Justin Lemkul <jalemkul at vt.edu> -----