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

Thu Jun 1 17:02:09 CEST 2017

Hi Mark,

Exactly. But we want to phrase it such that it is legible in the legend if the file is plotted.

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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