[gmx-users] column no 1 , 2 and 3? of " hbnum.xvg " file? Re: gromacs.org_gmx-users Digest, Vol 157, Issue 135
David van der Spoel
spoel at xray.bmc.uu.se
Sun May 28 11:17:46 CEST 2017
On 28/05/17 09:30, Adarsh V. K. wrote:
> So how can we conclude about column no 1 , 2 and 3 of " hbnum.xvg " file?
As it says in the legend:
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
Note that s1 does NOT include s0.
>
> 2. Re: Third column of the " hbnum.xvg " file?...What is it
>> meant for ? (Erik Marklund)
>> 3. Re: Third column of the " hbnum.xvg " file?...What is it
>> meant for ? (Justin Lemkul)
>> -----------------------------------------------------
>>
>> Message: 2
>> Date: Sat, 27 May 2017 18:44:19 +0000
>> From: Erik Marklund <erik.marklund at kemi.uu.se>
>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
>> file?...What is it meant for ?
>>
>> Hi Mark,
>>
>> Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.
>>
>> 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 ? 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>
>> -------------------------------------------------------------------------------------
>>
>> Message: 3
>> Date: Sat, 27 May 2017 14:46:21 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Third column of the " hbnum.xvg "
>> file?...What is it meant for ?
>> Message-ID: <0cbf8255-3416-b725-7afd-87d44290576f at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>> On 5/27/17 2:44 PM, Erik Marklund wrote:
>>> Hi Mark,
>>>
>>> Thinking out loud: ?Non-Hbonding pairs within 3.5 ??.
>>>
>>
>> I think it should be more explicit, and exactly what we always tell people:
>>
>> -num: number of hydrogen bonds as a function of time. The second column
>> contains the number of atom pairs that satisfy the distance criterion but
>> not
>> the angle criterion for hydrogen bonding.
>>
>> -Justin
>>
>>> 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 ? 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
>>
>> ==================================================
>>
--
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
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