Re: [gmx-users] Re: g_analyze

2013-11-12 Thread Justin Lemkul



On 11/12/13 8:33 AM, bharat gupta wrote:

Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.



Because that's not the function of g_analyze.  Use trjconv -dump with a suitable 
index file (from g_select).


-Justin



On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul  wrote:




On 11/11/13 6:56 PM, bharat gupta wrote:


Hi,

I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?



Start with g_select -select 'help all' and see what you can determine.
  Such selections are rather straightforward and have been explained several
times on the list.  If you need help, show us what you're doing and
describe why it isn't what you want.  It will ultimately save a lot of time.

-Justin




On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta 
wrote:

  Sorry, I attached the wrong file . Here's the average file generate from

one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does
then
the average file or its graph tells ??



On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul  wrote:




On 11/11/13 4:06 AM, bharat gupta wrote:

  In addition to my previous question, I have another question about

g_analyze. When I used the hbond.xvg file to get the average and
plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives
7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

 std. dev.relative deviation of
  standard   -   cumulants from
those
of
set  average   deviation  sqrt(n-1)   a Gaussian
distribition
 cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg


  Neither of these files produce output that corresponds to the PNG

image
above. Both files have values in 6-9 H-bond range and thus agree with
the
g_analyze output, which I can reproduce.  I suspect you're somehow
getting
your files mixed up.


-Justin


  On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta <

bharat.85.m...@gmail.com>
wrote:

   thank you informing about g_rdf...



Is it possible to dump the structure with those average water
molecules
interacting with the residues. I generated the hbond.log file which
gives
the details but I need to generate a figure for this ??



On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul 
wrote:




On 11/10/13 8:38 PM, bharat gupta wrote:

   But trjorder can be used to calculate the hydration layer or shell


around
residues ... Right ??


   Yes, but I also tend to think that integrating an RDF is also a
more


straightforward way of doing that.  With trjorder, you set some
arbitrary
cutoff that may or may not be an informed decision - with an RDF it
is
clear where the hydration layers are.

-Justin



   On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul 


wrote:



  On 11/10/13 8:30 PM, bharat gupta wrote:


Thanks for your reply. I was missing the scientific notation
part.
Now

  everything is fine.


Regarding trjorder, it doesn't measure h-bonds but gives the water
nearest
to protein.


I wouldn't try to draw any sort of comparison between the
output
of

  trjorder and g_hbond.  If you want to measure H-bonds, there's

only
one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Searc

Re: [gmx-users] Re: g_analyze

2013-11-12 Thread bharat gupta
Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.


On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul  wrote:

>
>
> On 11/11/13 6:56 PM, bharat gupta wrote:
>
>> Hi,
>>
>> I tried g_select to dump the structure with the interacting water
>> molecules, but I don't know know how to do that. I searched for some
>> threads in the discussion but wasn't able to find anything related to my
>> need. Can you explain how can I do that ?
>>
>>
> Start with g_select -select 'help all' and see what you can determine.
>  Such selections are rather straightforward and have been explained several
> times on the list.  If you need help, show us what you're doing and
> describe why it isn't what you want.  It will ultimately save a lot of time.
>
> -Justin
>
>
>
>> On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta 
>> wrote:
>>
>>  Sorry, I attached the wrong file . Here's the average file generate from
>>> one of the files I sent in my last mail. I used the command g_analyze -f
>>> hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
>>> from this command :-
>>>
>>> https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg
>>>
>>> Now, if you see, the graph (in previous mail) and average file, both
>>> correlates well. I have a doubt about interpreting the result from
>>> g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
>>> bonds are formed during the simulation time of 5ns to 10ns. What does
>>> then
>>> the average file or its graph tells ??
>>>
>>>
>>>
>>> On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul  wrote:
>>>
>>>

 On 11/11/13 4:06 AM, bharat gupta wrote:

  In addition to my previous question, I have another question about
> g_analyze. When I used the hbond.xvg file to get the average and
> plotted
> the average.xvg file I found that the average value is round 4 to 5
> according to the graph. But g_analyze in its final calculation gives
> 7.150
> as the average values... Here's the link for the graph and result of
> average value calculated by g_analyze :-
>
> std. dev.relative deviation of
>  standard   -   cumulants from
> those
> of
> set  average   deviation  sqrt(n-1)   a Gaussian
> distribition
> cum. 3   cum. 4
> SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
>
> SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153
>
> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
>
> Here's the  link hbond.xvg file and its averaged file
> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>
>
>  Neither of these files produce output that corresponds to the PNG
 image
 above. Both files have values in 6-9 H-bond range and thus agree with
 the
 g_analyze output, which I can reproduce.  I suspect you're somehow
 getting
 your files mixed up.


 -Justin


  On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta <
> bharat.85.m...@gmail.com>
> wrote:
>
>   thank you informing about g_rdf...
>
>>
>> Is it possible to dump the structure with those average water
>> molecules
>> interacting with the residues. I generated the hbond.log file which
>> gives
>> the details but I need to generate a figure for this ??
>>
>>
>>
>> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul 
>> wrote:
>>
>>
>>
>>> On 11/10/13 8:38 PM, bharat gupta wrote:
>>>
>>>   But trjorder can be used to calculate the hydration layer or shell
>>>
 around
 residues ... Right ??


   Yes, but I also tend to think that integrating an RDF is also a
 more

>>> straightforward way of doing that.  With trjorder, you set some
>>> arbitrary
>>> cutoff that may or may not be an informed decision - with an RDF it
>>> is
>>> clear where the hydration layers are.
>>>
>>> -Justin
>>>
>>>
>>>
>>>   On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul 
>>>
 wrote:



  On 11/10/13 8:30 PM, bharat gupta wrote:
>
>Thanks for your reply. I was missing the scientific notation
> part.
> Now
>
>  everything is fine.
>>
>> Regarding trjorder, it doesn't measure h-bonds but gives the water
>> nearest
>> to protein.
>>
>>
>>I wouldn't try to draw any sort of comparison between the
>> output
>> of
>>

Re: [gmx-users] Re: g_analyze

2013-11-12 Thread Justin Lemkul



On 11/11/13 6:56 PM, bharat gupta wrote:

Hi,

I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?



Start with g_select -select 'help all' and see what you can determine.  Such 
selections are rather straightforward and have been explained several times on 
the list.  If you need help, show us what you're doing and describe why it isn't 
what you want.  It will ultimately save a lot of time.


-Justin



On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta wrote:


Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??



On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul  wrote:




On 11/11/13 4:06 AM, bharat gupta wrote:


In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives
7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

std. dev.relative deviation of
 standard   -   cumulants from those
of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg



Neither of these files produce output that corresponds to the PNG image
above. Both files have values in 6-9 H-bond range and thus agree with the
g_analyze output, which I can reproduce.  I suspect you're somehow getting
your files mixed up.


-Justin



On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta 
wrote:

  thank you informing about g_rdf...


Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which
gives
the details but I need to generate a figure for this ??



On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul 
wrote:




On 11/10/13 8:38 PM, bharat gupta wrote:

  But trjorder can be used to calculate the hydration layer or shell

around
residues ... Right ??


  Yes, but I also tend to think that integrating an RDF is also a more

straightforward way of doing that.  With trjorder, you set some
arbitrary
cutoff that may or may not be an informed decision - with an RDF it is
clear where the hydration layers are.

-Justin



  On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul 

wrote:




On 11/10/13 8:30 PM, bharat gupta wrote:

   Thanks for your reply. I was missing the scientific notation part.
Now


everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water
nearest
to protein.


   I wouldn't try to draw any sort of comparison between the output
of


trjorder and g_hbond.  If you want to measure H-bonds, there's only
one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


  --

==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.u

Re: [gmx-users] Re: g_analyze

2013-11-12 Thread Justin Lemkul



On 11/11/13 5:39 PM, bharat gupta wrote:

Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??



It's an average over sets.  It is not equivalent to the output printed to the 
screen, nor is it supposed to.  The value printed to the screen is the actual 
average of the data set of interest, as is intuitive from your values.  An 
average of 4 is impossible if all the data points are in the range of 6-9.


-Justin




On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul  wrote:




On 11/11/13 4:06 AM, bharat gupta wrote:


In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

std. dev.relative deviation of
 standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163

SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg



Neither of these files produce output that corresponds to the PNG image
above. Both files have values in 6-9 H-bond range and thus agree with the
g_analyze output, which I can reproduce.  I suspect you're somehow getting
your files mixed up.


-Justin



On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta 
wrote:

  thank you informing about g_rdf...


Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??



On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:




On 11/10/13 8:38 PM, bharat gupta wrote:

  But trjorder can be used to calculate the hydration layer or shell

around
residues ... Right ??


  Yes, but I also tend to think that integrating an RDF is also a more

straightforward way of doing that.  With trjorder, you set some
arbitrary
cutoff that may or may not be an informed decision - with an RDF it is
clear where the hydration layers are.

-Justin



  On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul 

wrote:




On 11/10/13 8:30 PM, bharat gupta wrote:

   Thanks for your reply. I was missing the scientific notation part.
Now


everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water
nearest
to protein.


   I wouldn't try to draw any sort of comparison between the output of


trjorder and g_hbond.  If you want to measure H-bonds, there's only
one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


  --

==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don'

Re: [gmx-users] Re: g_analyze

2013-11-12 Thread bharat gupta
Hi,

I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?


On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta wrote:

> Sorry, I attached the wrong file . Here's the average file generate from
> one of the files I sent in my last mail. I used the command g_analyze -f
> hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
> from this command :-
>
> https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg
>
> Now, if you see, the graph (in previous mail) and average file, both
> correlates well. I have a doubt about interpreting the result from
> g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
> bonds are formed during the simulation time of 5ns to 10ns. What does then
> the average file or its graph tells ??
>
>
>
> On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/11/13 4:06 AM, bharat gupta wrote:
>>
>>> In addition to my previous question, I have another question about
>>> g_analyze. When I used the hbond.xvg file to get the average and plotted
>>> the average.xvg file I found that the average value is round 4 to 5
>>> according to the graph. But g_analyze in its final calculation gives
>>> 7.150
>>> as the average values... Here's the link for the graph and result of
>>> average value calculated by g_analyze :-
>>>
>>>std. dev.relative deviation of
>>> standard   -   cumulants from those
>>> of
>>> set  average   deviation  sqrt(n-1)   a Gaussian distribition
>>>cum. 3   cum. 4
>>> SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
>>>
>>> SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153
>>>
>>> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
>>>
>>> Here's the  link hbond.xvg file and its averaged file
>>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>>
>>>
>> Neither of these files produce output that corresponds to the PNG image
>> above. Both files have values in 6-9 H-bond range and thus agree with the
>> g_analyze output, which I can reproduce.  I suspect you're somehow getting
>> your files mixed up.
>>
>>
>> -Justin
>>
>>
>>> On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta 
>>> wrote:
>>>
>>>  thank you informing about g_rdf...

 Is it possible to dump the structure with those average water molecules
 interacting with the residues. I generated the hbond.log file which
 gives
 the details but I need to generate a figure for this ??



 On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul 
 wrote:


>
> On 11/10/13 8:38 PM, bharat gupta wrote:
>
>  But trjorder can be used to calculate the hydration layer or shell
>> around
>> residues ... Right ??
>>
>>
>>  Yes, but I also tend to think that integrating an RDF is also a more
> straightforward way of doing that.  With trjorder, you set some
> arbitrary
> cutoff that may or may not be an informed decision - with an RDF it is
> clear where the hydration layers are.
>
> -Justin
>
>
>
>  On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul 
>> wrote:
>>
>>
>>
>>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>>
>>>   Thanks for your reply. I was missing the scientific notation part.
>>> Now
>>>
 everything is fine.

 Regarding trjorder, it doesn't measure h-bonds but gives the water
 nearest
 to protein.


   I wouldn't try to draw any sort of comparison between the output
 of

>>> trjorder and g_hbond.  If you want to measure H-bonds, there's only
>>> one
>>> tool for that.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>>
>>> ==
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't 

Re: [gmx-users] Re: g_analyze

2013-11-12 Thread bharat gupta
Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??



On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul  wrote:

>
>
> On 11/11/13 4:06 AM, bharat gupta wrote:
>
>> In addition to my previous question, I have another question about
>> g_analyze. When I used the hbond.xvg file to get the average and plotted
>> the average.xvg file I found that the average value is round 4 to 5
>> according to the graph. But g_analyze in its final calculation gives 7.150
>> as the average values... Here's the link for the graph and result of
>> average value calculated by g_analyze :-
>>
>>std. dev.relative deviation of
>> standard   -   cumulants from those of
>> set  average   deviation  sqrt(n-1)   a Gaussian distribition
>>cum. 3   cum. 4
>> SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
>>
>> SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153
>>
>> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
>>
>> Here's the  link hbond.xvg file and its averaged file
>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>
>>
> Neither of these files produce output that corresponds to the PNG image
> above. Both files have values in 6-9 H-bond range and thus agree with the
> g_analyze output, which I can reproduce.  I suspect you're somehow getting
> your files mixed up.
>
>
> -Justin
>
>
>> On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta 
>> wrote:
>>
>>  thank you informing about g_rdf...
>>>
>>> Is it possible to dump the structure with those average water molecules
>>> interacting with the residues. I generated the hbond.log file which gives
>>> the details but I need to generate a figure for this ??
>>>
>>>
>>>
>>> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:
>>>
>>>

 On 11/10/13 8:38 PM, bharat gupta wrote:

  But trjorder can be used to calculate the hydration layer or shell
> around
> residues ... Right ??
>
>
>  Yes, but I also tend to think that integrating an RDF is also a more
 straightforward way of doing that.  With trjorder, you set some
 arbitrary
 cutoff that may or may not be an informed decision - with an RDF it is
 clear where the hydration layers are.

 -Justin



  On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul 
> wrote:
>
>
>
>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>
>>   Thanks for your reply. I was missing the scientific notation part.
>> Now
>>
>>> everything is fine.
>>>
>>> Regarding trjorder, it doesn't measure h-bonds but gives the water
>>> nearest
>>> to protein.
>>>
>>>
>>>   I wouldn't try to draw any sort of comparison between the output of
>>>
>> trjorder and g_hbond.  If you want to measure H-bonds, there's only
>> one
>> tool for that.
>>
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>  --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 

Re: [gmx-users] Re: g_analyze

2013-11-11 Thread Justin Lemkul



On 11/11/13 4:06 AM, bharat gupta wrote:

In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

   std. dev.relative deviation of
standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg



Neither of these files produce output that corresponds to the PNG image above. 
Both files have values in 6-9 H-bond range and thus agree with the g_analyze 
output, which I can reproduce.  I suspect you're somehow getting your files 
mixed up.


-Justin



On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote:


thank you informing about g_rdf...

Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??



On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:




On 11/10/13 8:38 PM, bharat gupta wrote:


But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??



Yes, but I also tend to think that integrating an RDF is also a more
straightforward way of doing that.  With trjorder, you set some arbitrary
cutoff that may or may not be an informed decision - with an RDF it is
clear where the hydration layers are.

-Justin




On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:




On 11/10/13 8:30 PM, bharat gupta wrote:

  Thanks for your reply. I was missing the scientific notation part. Now

everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water
nearest
to protein.


  I wouldn't try to draw any sort of comparison between the output of

trjorder and g_hbond.  If you want to measure H-bonds, there's only one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Re: g_analyze

2013-11-11 Thread Justin Lemkul



On 11/11/13 1:30 AM, bharat gupta wrote:

thank you informing about g_rdf...

Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??



g_select

-Justin



On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:




On 11/10/13 8:38 PM, bharat gupta wrote:


But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??



Yes, but I also tend to think that integrating an RDF is also a more
straightforward way of doing that.  With trjorder, you set some arbitrary
cutoff that may or may not be an informed decision - with an RDF it is
clear where the hydration layers are.

-Justin




On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:




On 11/10/13 8:30 PM, bharat gupta wrote:

  Thanks for your reply. I was missing the scientific notation part. Now

everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water
nearest
to protein.


  I wouldn't try to draw any sort of comparison between the output of

trjorder and g_hbond.  If you want to measure H-bonds, there's only one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: g_analyze

2013-11-11 Thread bharat gupta
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-

  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1  * 7.150740e+00 *  8.803173e-01   1.760635e-02   0.0620.163
SS2   1.490604e+00   1.164761e+00   2.329523e-02   0.4950.153

https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png

Here's the  link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg


On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta wrote:

> thank you informing about g_rdf...
>
> Is it possible to dump the structure with those average water molecules
> interacting with the residues. I generated the hbond.log file which gives
> the details but I need to generate a figure for this ??
>
>
>
> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/10/13 8:38 PM, bharat gupta wrote:
>>
>>> But trjorder can be used to calculate the hydration layer or shell around
>>> residues ... Right ??
>>>
>>>
>> Yes, but I also tend to think that integrating an RDF is also a more
>> straightforward way of doing that.  With trjorder, you set some arbitrary
>> cutoff that may or may not be an informed decision - with an RDF it is
>> clear where the hydration layers are.
>>
>> -Justin
>>
>>
>>
>>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:
>>>
>>>

 On 11/10/13 8:30 PM, bharat gupta wrote:

  Thanks for your reply. I was missing the scientific notation part. Now
> everything is fine.
>
> Regarding trjorder, it doesn't measure h-bonds but gives the water
> nearest
> to protein.
>
>
>  I wouldn't try to draw any sort of comparison between the output of
 trjorder and g_hbond.  If you want to measure H-bonds, there's only one
 tool for that.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/Search before posting!
 * Please don't post (un)subscribe requests to the list. Use the www
 interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread bharat gupta
thank you informing about g_rdf...

Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??


On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul  wrote:

>
>
> On 11/10/13 8:38 PM, bharat gupta wrote:
>
>> But trjorder can be used to calculate the hydration layer or shell around
>> residues ... Right ??
>>
>>
> Yes, but I also tend to think that integrating an RDF is also a more
> straightforward way of doing that.  With trjorder, you set some arbitrary
> cutoff that may or may not be an informed decision - with an RDF it is
> clear where the hydration layers are.
>
> -Justin
>
>
>
>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>>
>>>  Thanks for your reply. I was missing the scientific notation part. Now
 everything is fine.

 Regarding trjorder, it doesn't measure h-bonds but gives the water
 nearest
 to protein.


  I wouldn't try to draw any sort of comparison between the output of
>>> trjorder and g_hbond.  If you want to measure H-bonds, there's only one
>>> tool for that.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>>
>>> ==
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread Justin Lemkul



On 11/10/13 8:38 PM, bharat gupta wrote:

But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??



Yes, but I also tend to think that integrating an RDF is also a more 
straightforward way of doing that.  With trjorder, you set some arbitrary cutoff 
that may or may not be an informed decision - with an RDF it is clear where the 
hydration layers are.


-Justin



On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:




On 11/10/13 8:30 PM, bharat gupta wrote:


Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.



I wouldn't try to draw any sort of comparison between the output of
trjorder and g_hbond.  If you want to measure H-bonds, there's only one
tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread bharat gupta
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??


On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul  wrote:

>
>
> On 11/10/13 8:30 PM, bharat gupta wrote:
>
>> Thanks for your reply. I was missing the scientific notation part. Now
>> everything is fine.
>>
>> Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
>> to protein.
>>
>>
> I wouldn't try to draw any sort of comparison between the output of
> trjorder and g_hbond.  If you want to measure H-bonds, there's only one
> tool for that.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread Justin Lemkul



On 11/10/13 8:30 PM, bharat gupta wrote:

Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.



I wouldn't try to draw any sort of comparison between the output of trjorder and 
g_hbond.  If you want to measure H-bonds, there's only one tool for that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread bharat gupta
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.

Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.




On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul  wrote:

>
>
> On 11/10/13 7:18 PM, bharat gupta wrote:
>
>> I checked the file hbnum.xvg file and it contains three columns - time,
>> hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
>>
>
> The third column is not actually H-bonds, then ;)
>
>
>  the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
>> column. Am I right here or not ??
>>
>>
> Yes.
>
>
>  I tried to calculate the h-bond for residues 115-118 individually, and
>> then
>> checked the average for each residue. For single residue calculation, the
>> g_analyze average value is correct.
>>
>> But when I calculate the h-bond as a range 115-118, I get the g_analyze
>> value as 1.62 . I calculated the average manually in excel, got the
>> average
>> values as 16.2 [which is (g_analyze avg value)/10].
>>
>>
> That is impossible.  You cannot get a different average by examining the
> same numbers.  Read the g_analyze output again - I am willing to bet that
> you're not seeing the exponent of the scientific notation.
>
>
>  I then added up the average values of h-bonds of individual residues and
>> the final comes around 16.2, same as that of the 115-118 range h-bonds.
>> This means that my calculation is correct.
>>
>> I also used trjorder to calculate h-bond at distance 0.34 for residues
>> 115-118. I got the average value around 2.51 from g_analyze, where as
>> manual calculation gives 25.1. I don't knw why for the range the g_analyze
>> give avg as (actual avg value)/10 ??
>>
>> Why does trjorder and g_hbond gives different number of hydrogen bonds for
>> the same residue set??
>>
>>
> All of this comes down to correctly reading the screen output.  I have no
> idea what you're doing with trjorder, though.  It doesn't measure H-bonds.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread Justin Lemkul



On 11/10/13 7:18 PM, bharat gupta wrote:

I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is


The third column is not actually H-bonds, then ;)


the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??



Yes.


I tried to calculate the h-bond for residues 115-118 individually, and then
checked the average for each residue. For single residue calculation, the
g_analyze average value is correct.

But when I calculate the h-bond as a range 115-118, I get the g_analyze
value as 1.62 . I calculated the average manually in excel, got the average
values as 16.2 [which is (g_analyze avg value)/10].



That is impossible.  You cannot get a different average by examining the same 
numbers.  Read the g_analyze output again - I am willing to bet that you're not 
seeing the exponent of the scientific notation.



I then added up the average values of h-bonds of individual residues and
the final comes around 16.2, same as that of the 115-118 range h-bonds.
This means that my calculation is correct.

I also used trjorder to calculate h-bond at distance 0.34 for residues
115-118. I got the average value around 2.51 from g_analyze, where as
manual calculation gives 25.1. I don't knw why for the range the g_analyze
give avg as (actual avg value)/10 ??

Why does trjorder and g_hbond gives different number of hydrogen bonds for
the same residue set??



All of this comes down to correctly reading the screen output.  I have no idea 
what you're doing with trjorder, though.  It doesn't measure H-bonds.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread bharat gupta
I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??

I tried to calculate the h-bond for residues 115-118 individually, and then
checked the average for each residue. For single residue calculation, the
g_analyze average value is correct.

But when I calculate the h-bond as a range 115-118, I get the g_analyze
value as 1.62 . I calculated the average manually in excel, got the average
values as 16.2 [which is (g_analyze avg value)/10].

I then added up the average values of h-bonds of individual residues and
the final comes around 16.2, same as that of the 115-118 range h-bonds.
This means that my calculation is correct.

I also used trjorder to calculate h-bond at distance 0.34 for residues
115-118. I got the average value around 2.51 from g_analyze, where as
manual calculation gives 25.1. I don't knw why for the range the g_analyze
give avg as (actual avg value)/10 ??

Why does trjorder and g_hbond gives different number of hydrogen bonds for
the same residue set??

Thanks
---
BHARAT



On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul  wrote:

>
>
> On 11/10/13 12:20 AM, bharat gupta wrote:
>
>> Hi,
>> I used the command g_hbond to find h-bond between  residues 115-118 and
>> water. Then I used g_analyze to find out the average and it gives the
>> value
>> for the hbonds like this :-
>>
>>std. dev.relative deviation of
>> standard   -   cumulants from those of
>> set  average   deviation  sqrt(n-1)   a Gaussian distribition
>>cum. 3   cum. 4
>> SS1   6.877249e-02   2.546419e-01   5.092839e-03   2.1813.495
>> SS2   6.997201e-02   2.673450e-01   5.346901e-03   2.4215.001
>>
>> When I calculated the average manually, by taking the average of numbers
>> in
>> second column of hbnum.xvg file, I got a value of around 13.5.. What is
>> the
>> reason for such a large difference.
>>
>>
> Hard to say, but I've never known g_analyze to be wrong, so I'd suspect
> something is amiss in your manual calculation.  The difference between 13.5
> and 0.0069 is huge; you should be able to scan through the data file to see
> what the expected value should be.
>
>
>  In another case, g_analyze gives avg values of aroun 6.9 for hbond between
>> two residues and when I calculated it maually I got the avg values as 6.8
>>
>>> ..
>>>
>>
>> Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time
>> and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond
>> analysis ??
>>
>
> Data sets 1 and 2.  You will note that there are two columns of data in
> the -hbnum output produced by g_hbond, with titles explaining both.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/Search before posting!
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>
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Re: [gmx-users] Re: g_analyze

2013-11-10 Thread Justin Lemkul



On 11/10/13 12:20 AM, bharat gupta wrote:

Hi,
I used the command g_hbond to find h-bond between  residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-

   std. dev.relative deviation of
standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4
SS1   6.877249e-02   2.546419e-01   5.092839e-03   2.1813.495
SS2   6.997201e-02   2.673450e-01   5.346901e-03   2.4215.001

When I calculated the average manually, by taking the average of numbers in
second column of hbnum.xvg file, I got a value of around 13.5.. What is the
reason for such a large difference.



Hard to say, but I've never known g_analyze to be wrong, so I'd suspect 
something is amiss in your manual calculation.  The difference between 13.5 and 
0.0069 is huge; you should be able to scan through the data file to see what the 
expected value should be.



In another case, g_analyze gives avg values of aroun 6.9 for hbond between
two residues and when I calculated it maually I got the avg values as 6.8

..


Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time
and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond
analysis ??


Data sets 1 and 2.  You will note that there are two columns of data in the 
-hbnum output produced by g_hbond, with titles explaining both.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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