[gmx-users] water mediated Hbond
spss4 at iacs.res.in
spss4 at iacs.res.in
Mon May 13 17:20:38 CEST 2019
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:
>> 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.
>> 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
>>> Gromacs Users mailing list
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
----- End message from Justin Lemkul <jalemkul at vt.edu> -----
More information about the gromacs.org_gmx-users