[gmx-users] water mediated Hbond

Fri May 17 07:30:16 CEST 2019

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

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