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.m...@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 <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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists