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

[Mark Abraham]

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 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>
> .
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