[gmx-users] DETECTING HYDROGEN BONDS

[Mark Abraham]

Hi,

Have a look at the legend text :-) First column is the time.

Mark

On Sat, 11 Feb 2017 12:12 Subashini .K <subashinik at hotmail.com> wrote:

> Thank you very much for the reply
>
>
> Wanted to know what the third column represents?
>
>
> The header was
>
>
> # gmx hbond is part of G R O M A C S:
> # # Glycine aRginine prOline Methionine Alanine Cystine Serine #
> @    title "Hydrogen Bonds"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Number"
> @TYPE xy @ view 0.15, 0.15, 0.75, 0.85
> @ legend on @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>
> Through molecular docking had obtained hydrogen bonding with GLU 387 AND
> GLU 389
>
> Wish to ascertain them through simulations too. How to do it?
>
> Thanks,
> Subashini.K
>
>
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alex <
> nedomacho at gmail.com>
> Sent: Saturday, February 11, 2017 1:45 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DETECTING HYDROGEN BONDS
>
> Not sure what you mean by "interpret these numbers," except that now we
> know that your simulation was 2 ns long.  The xvg file contains a
> header, which describes what each column is. If I recall correctly, the
> second column is the number of hbonds according to the default search
> cutoff. The first column is your simulated time in ps.
>
> Alex
>
>
> On 2/11/2017 1:00 AM, Subashini .K wrote:
> > Hi gromacs users,
> >
> >
> > After protein ligand simulations, gave the following command to detect
> hydrogen bond
> >
> >
> > gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg
> >
> > After selecting protein and ligand
> >
> >
> > Obtained the following result
> >
> >
> > I am a beginner. Could someone help me  to interpret these numbers? The
> simulation was done for 2 ns
> >
> >
> >
> >                  0           2           1
> >
> >                100           2           1
> >
> >                 200           1           0
> >
> >                 300           1           0
> >
> >                 400           1           0
> >
> >                 500           1           0
> >
> >                 600           1           0
> >
> >                700           1           0
> >
> >                800           0           0
> >
> >                900           1           0
> >
> >             1000           1           0
> >
> >              1100           1           0
> >
> >           1200           1           0
> >
> >           1300           0           2
> >
> >          1400           1           0
> >
> >           1500           1           0
> >
> >           1600           1           0
> >
> >            1700           1           0
> >
> >           1800           0           1
> >
> >            1900           1           0
> >
> >           2000           1           0
> >
> >
> > Thanks,
> >
> > Subashini.K
>
>
> --
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