[gmx-users] Re: g_analyze
bharat gupta
bharat.85.monu at gmail.com
Tue Nov 12 00:56:25 CET 2013
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 ?
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
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>> Support/Mailing_Lists/Search before posting!
>>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at http://www.gromacs.org/
>>>>> Support/Mailing_Lists/Search before posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
>
More information about the gromacs.org_gmx-users
mailing list