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

2017-06-01 Thread Justin Lemkul 



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 
> 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 
>
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 
> 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 
>
wrote:



On 26 May 2017, at 22:12, David van der Spoel 

> 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. 

> 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"
  02   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> <018-471%2042%2005>
.
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-06-01 Thread Erik Marklund 
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 
> 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 
>
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 
> 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 
>
wrote:



On 26 May 2017, at 22:12, David van der Spoel 

> 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. 

> 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"
 02   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> <018-471%2042%2005>
.
http://www.icm.uu.se
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-06-01 Thread Erik Marklund 
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  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 
> wrote:
> 
>> 
>> 
>> On 26 May 2017, at 22:12, David van der Spoel > > 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. > > 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"
>>   02   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
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org> gmx-users-requ...@gromacs.org>.
>> 
>> 
>> 
>> --
>> 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>
>> .
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
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>> send a mail to gmx-users-requ...@gromacs.org> gmx-users-requ...@gromacs.org>.
>> 
>> --
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-06-01 Thread Mark Abraham 
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 
wrote:

>
>
> On 26 May 2017, at 22:12, David van der Spoel  > 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.  > 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"
>02   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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org>.
>
>
>
> --
> 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>
> .
> http://www.icm.uu.se
> --
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-27 Thread Justin Lemkul 



On 5/27/17 2:44 PM, Erik Marklund wrote:

Hi Mark,

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



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  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 
wrote:




On 26 May 2017, at 22:12, David van der Spoel > 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. > 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"
   02   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>
.
http://www.icm.uu.se
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

2017-05-27 Thread 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  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 
> wrote:
> 
>> 
>> 
>> On 26 May 2017, at 22:12, David van der Spoel > > 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. > > 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"
>>   02   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
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org> gmx-users-requ...@gromacs.org>.
>> 
>> 
>> 
>> --
>> 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>
>> .
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org> gmx-users-requ...@gromacs.org>.
>> 
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>> * Please search the archive at
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-27 Thread Mark Abraham 
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 
wrote:

>
>
> On 26 May 2017, at 22:12, David van der Spoel  > 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.  > 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"
>02   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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org>.
>
>
>
> --
> 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>
> .
> http://www.icm.uu.se
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-27 Thread Erik Marklund 


On 26 May 2017, at 22:12, David van der Spoel 
> 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. 
> 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"
   02   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
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread David van der Spoel 

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.


Kind regards,
Erik


On 26 May 2017, at 19:38, Adarsh V. K.  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"
02   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
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread Erik Marklund 
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is 
why they are sometimes fewer than the hbonds.

Kind regards,
Erik

> On 26 May 2017, at 19:38, Adarsh V. K.  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"
> 02   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
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
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[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-05-26 Thread Adarsh V. K. 
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"
 02   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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