Thank you for your kind reply.
- Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
Date: Fri, 17 May 2019 13:33:30 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hb
---
> Date: Tue, 14 May 2019 19:21:19 +0530
> From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] water mediated Hbond
> To: gmx-us...@gromacs.org
>
> > Hi
> >In md analysis y
from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -
Date: Tue, 14 May 2019 19:21:19 +0530
From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
To: gmx-us...@gromacs.org
Hi
In md
1 +0530
>> From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
>> Reply-To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] water mediated Hbond
>> To: gmx-us...@gromacs.org
>>
>> > The lifetime of the h-bond can be calculated by calculating
tk.edu.in>
> -
> Date: Mon, 13 May 2019 22:24:51 +0530
> From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] water mediated Hbond
> To: gmx-us...@gromacs.org
>
> > The lifetime of th
ht way to proceed?
- Message from Justin Lemkul -
Date: Mon, 13 May 2019 09:10:41 -0400
From: Justin Lemkul
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
To: gmx-us...@gromacs.org
On 5/13/19 8:48 AM, Bratin Kumar Das wrote:
Hi,
You ca
Subject: Re: [gmx-users] water mediated Hbond
To: gmx-us...@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 whi
gt;
> - Message from Justin Lemkul -
> Date: Mon, 13 May 2019 09:10:41 -0400
> From: Justin Lemkul
> Reply-To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] water mediated Hbond
> To: gmx-us...@gromacs.org
>
> > On 5/13/19 8:48 AM, Bratin Kumar Das
May 2019 09:10:41 -0400
From: Justin Lemkul
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
To: gmx-us...@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
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 simul
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
On Tue 7 May, 2019, 12:40 PM , wrote:
> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecu
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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