[gmx-users] Re: g_analyze

Justin Lemkul jalemkul at vt.edu
Tue Nov 12 14:14:35 CET 2013 


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 <jalemkul at vt.edu> 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       0.062    0.163
>>>
>>> SS2   1.490604e+00   1.164761e+00   2.329523e-02       0.495    0.153
>>>
>>> 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.monu at 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 <jalemkul at vt.edu> 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 <jalemkul at vt.edu>
>>>>>> 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
>>>>>>>
>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>
>>>>>>> ==================================================
>>>>>>> --
>>>>>>> gmx-users mailing list    gmx-users at 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-request at 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
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at 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-request at 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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
>> --
>> gmx-users mailing list    gmx-users at 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-request at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================

More information about the gromacs.org_gmx-users mailing list