[gmx-users] water mediated Hbond

[spss4 at iacs.res.in]

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