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

[Erik Marklund]

Hi Mark,

Thinking out loud: “Non-Hbonding pairs within 3.5 Å”.

Kind regards,
Erik

> On 27 May 2017, at 17:56, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> 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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