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

[Erik Marklund]

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.
http://www.icm.uu.se<http://www.icm.uu.se/>
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