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. On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/10/13 7:18 PM, bharat gupta wrote: > >> I checked the file hbnum.xvg file and it contains three columns - time, >> hbonds, hbonds that donot follow the angle criteria. In that case SS1 is >> > > The third column is not actually H-bonds, then ;) > > > the average of actual hbonds (2nd column ) and SS2 is the average of 3rd >> column. Am I right here or not ?? >> >> > Yes. > > > I tried to calculate the h-bond for residues 115-118 individually, and >> then >> checked the average for each residue. For single residue calculation, the >> g_analyze average value is correct. >> >> But when I calculate the h-bond as a range 115-118, I get the g_analyze >> value as 1.62 . I calculated the average manually in excel, got the >> average >> values as 16.2 [which is (g_analyze avg value)/10]. >> >> > That is impossible. You cannot get a different average by examining the > same numbers. Read the g_analyze output again - I am willing to bet that > you're not seeing the exponent of the scientific notation. > > > I then added up the average values of h-bonds of individual residues and >> the final comes around 16.2, same as that of the 115-118 range h-bonds. >> This means that my calculation is correct. >> >> I also used trjorder to calculate h-bond at distance 0.34 for residues >> 115-118. I got the average value around 2.51 from g_analyze, where as >> manual calculation gives 25.1. I don't knw why for the range the g_analyze >> give avg as (actual avg value)/10 ?? >> >> Why does trjorder and g_hbond gives different number of hydrogen bonds for >> the same residue set?? >> >> > All of this comes down to correctly reading the screen output. I have no > idea what you're doing with trjorder, though. It doesn't measure H-bonds. > > > -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 firstname.lastname@example.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 email@example.com 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