[gmx-users] Re: g_analyze

bharat gupta bharat.85.monu at gmail.com
Mon Nov 11 23:39:59 CET 2013


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
>>>>
>>>> ==================================================
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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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