[gmx-users] Re: g_analyze

[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       0.062    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

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