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.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 >> > > > > -- 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