[gmx-users] water mediated Hbond

Fri May 17 14:00:35 CEST 2019

  Thank you for your kind reply.
----- Message from Bratin Kumar Das <177cy500.bratin at nitk.edu.in> ---------
    Date: Fri, 17 May 2019 13:33:30 +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,
>    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
>> Office: 301 Fralin Hall
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