[gmx-users] column no 1 , 2 and 3? of " hbnum.xvg " file? Re: gromacs.org_gmx-users Digest, Vol 157, Issue 135

Adarsh V. K. adarsh_p130085bt at nitc.ac.in
Sun May 28 09:30:35 CEST 2017


So how can we conclude about column no 1 , 2 and 3 of " hbnum.xvg " file?

   2. Re: Third column of the " hbnum.xvg " file?...What is it
>       meant for ? (Erik Marklund)
>    3. Re: Third column of the " hbnum.xvg " file?...What is it
>       meant for ? (Justin Lemkul)
> -----------------------------------------------------
>
> Message: 2
> Date: Sat, 27 May 2017 18:44:19 +0000
> From: Erik Marklund <erik.marklund at kemi.uu.se>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
>         file?...What is it meant for ?
>
> Hi Mark,
>
> Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.
>
> Kind regards,
> Erik
>
> > On 27 May 2017, at 17:56, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >
> > Hi,
> >
> > So what should we document in the help text as the meaning, so we don't
> > keep having emails about this?
> >
> > Mark
> >
> > On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.marklund at kemi.uu.se>
> > wrote:
> >
> >>
> >>
> >> On 26 May 2017, at 22:12, David van der Spoel <spoel at xray.bmc.uu.se
> >> <mailto:spoel at xray.bmc.uu.se>> wrote:
> >>
> >> On 26/05/17 22:05, Erik Marklund wrote:
> >> ?Pairs within 0.35 nm?. They also don?t fulfil the angle criterion,
> which
> >> is why they are sometimes fewer than the hbonds.
> >>
> >> Therefore I would assume they are more instead.
> >>
> >>
> >> They sometimes are, but not necessarily. I pointed it out because
> >> sometimes people ask if g_hbond is buggy when they see that there are
> >> occasionally lower numbers in the third column, assuming that it
> contains
> >> all pairs within 3.5 ? regardless of angle which should more numeorus
> than
> >> the pairs that also fullfil the angle criterion. That?s not the meaning
> of
> >> the third column however.
> >>
> >> Kind regards,
> >> Erik
> >>
> >> On 26 May 2017, at 19:38, Adarsh V. K. <adarsh_p130085bt at nitc.ac.in
> >> <mailto:adarsh_p130085bt at nitc.ac.in>> wrote:
> >>
> >> Dear all,
> >>
> >> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
> >>
> >> I would like to edit the file before viewing in 'Xmgrace'
> >>
> >> I opened the hbnum.xvg using 'gedit'. It shows following details (see
> >> below)
> >>
> >> Can you please tell me what is there in the third column of the file?
> >>
> >> ---------------------------------------------------------
> >> # gmx hbond is part of G R O M A C S:
> >> #
> >> # GROtesk MACabre and Sinister
> >> #
> >> @    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"
> >>       0            2           7
> >>      10           2           5
> >>      20           4           3
> >>      30           3           2
> >>      40           3           3
> >>      50           5           1
> >>      60           3           6
> >>      70           3           6
> >>      80           2           3
> >>      90           5           1
> >>     100          3           3
> >> --
> >> Gromacs Users mailing list
> >>
>
> -------------------------------------------------------------------------------------
>
> Message: 3
> Date: Sat, 27 May 2017 14:46:21 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
>         file?...What is it meant for ?
> Message-ID: <0cbf8255-3416-b725-7afd-87d44290576f at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> On 5/27/17 2:44 PM, Erik Marklund wrote:
> > Hi Mark,
> >
> > Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.
> >
>
> I think it should be more explicit, and exactly what we always tell people:
>
> -num:  number of hydrogen bonds as a function of time. The second column
> contains the number of atom pairs that satisfy the distance criterion but
> not
> the angle criterion for hydrogen bonding.
>
> -Justin
>
> > Kind regards,
> > Erik
> >
> >> On 27 May 2017, at 17:56, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> So what should we document in the help text as the meaning, so we don't
> >> keep having emails about this?
> >>
> >> Mark
> >>
> >> On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.marklund at kemi.uu.se
> >
> >> wrote:
> >>
> >>>
> >>>
> >>> On 26 May 2017, at 22:12, David van der Spoel <spoel at xray.bmc.uu.se
> >>> <mailto:spoel at xray.bmc.uu.se>> wrote:
> >>>
> >>> On 26/05/17 22:05, Erik Marklund wrote:
> >>> ?Pairs within 0.35 nm?. They also don?t fulfil the angle criterion,
> which
> >>> is why they are sometimes fewer than the hbonds.
> >>>
> >>> Therefore I would assume they are more instead.
> >>>
> >>>
> >>> They sometimes are, but not necessarily. I pointed it out because
> >>> sometimes people ask if g_hbond is buggy when they see that there are
> >>> occasionally lower numbers in the third column, assuming that it
> contains
> >>> all pairs within 3.5 ? regardless of angle which should more numeorus
> than
> >>> the pairs that also fullfil the angle criterion. That?s not the
> meaning of
> >>> the third column however.
> >>>
> >>> Kind regards,
> >>> Erik
> >>>
> >>> On 26 May 2017, at 19:38, Adarsh V. K. <adarsh_p130085bt at nitc.ac.in
> >>> <mailto:adarsh_p130085bt at nitc.ac.in>> wrote:
> >>>
> >>> Dear all,
> >>>
> >>> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
> >>>
> >>> I would like to edit the file before viewing in 'Xmgrace'
> >>>
> >>> I opened the hbnum.xvg using 'gedit'. It shows following details (see
> >>> below)
> >>>
> >>> Can you please tell me what is there in the third column of the file?
> >>>
> >>> ---------------------------------------------------------
> >>> # gmx hbond is part of G R O M A C S:
> >>> #
> >>> # GROtesk MACabre and Sinister
> >>> #
> >>> @    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"
> >>>        0            2           7
> >>>       10           2           5
> >>>       20           4           3
> >>>       30           3           2
> >>>       40           3           3
> >>>       50           5           1
> >>>       60           3           6
> >>>       70           3           6
> >>>       80           2           3
> >>>       90           5           1
> >>>      100          3           3
>
> ==================================================
>


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