[gmx-users] Re: g_analyze
Justin Lemkul
jalemkul at vt.edu
Tue Nov 12 14:45:21 CET 2013
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 <jalemkul at vt.edu> 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 <bharat.85.monu at gmail.com>
>>> 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 <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
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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
>>>>>>>>
>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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