[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Mark Abraham]

Hi,

"Pairs within 0.35" has misled David, Justin and I, and doubtless others...
without clarification, it is normal to assume that if a hydrogen bond is
"pairs within 0.35 nm and a suitable angle," then "pairs within 0.35" would
be a superset of the former. But the field is actually "pairs within 0.35
that do not satisfy the angle requirement."

Mark

On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> Yes. The sets have no overlap. But for some reason putting that in a short
> description seems difficult :-)
>
> > On 1 Jun 2017, at 15:31, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >
> > Hi,
> >
> > I still don't understand your description. Is the third column
> *additional*
> > pairs within 0.35 that do not satisfy the angle criterion?
> >
> > 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 Å 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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> >>
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Head of Department, Cell & Molecular Biology, Uppsala University.
> >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205
> <018-471%2042%2005> <018-471%2042%2005>
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