[gmx-users] Re: g_analyze

[bharat gupta]

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


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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>
>
>
>