[gmx-users] Re: g_analyze
bharat gupta
bharat.85.monu at gmail.com
Tue Nov 12 14:33:03 CET 2013
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 <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
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>> --
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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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