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 <jalem...@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.m...@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 <jalem...@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 <jalem...@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 >>>>>> >>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>> >>>>>> ================================================== >>>>>> -- >>>>>> gmx-users mailing list gmx-users@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-requ...@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 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> >>>> ================================================== >>>> -- >>>> gmx-users mailing list gmx-users@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-requ...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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. 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