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

Thu Jun 1 17:06:24 CEST 2017

On 6/1/17 11:02 AM, Erik Marklund wrote:
> Hi Mark,
> 
> Exactly. But we want to phrase it such that it is legible in the legend if the file is plotted.
> 

I think we should adjust the help description in a manner like I suggested 
before (or more verbose if needed) and perhaps change the legend to "Non 
H-bonding atom pairs within 0.35 nm" to clearly indicate that the two columns 
are different quantities.

-Justin

> Erik
> 
> On 1 Jun 2017, at 16:51, Mark Abraham <mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com>> wrote:
> 
> 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<mailto: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<mailto: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<mailto: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>
> <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>
> <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.
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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