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 average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ??
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]. 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?? Thanks ----------- BHARAT On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/10/13 12:20 AM, bharat gupta wrote: > >> Hi, >> I used the command g_hbond to find h-bond between residues 115-118 and >> water. Then I used g_analyze to find out the average and it gives the >> value >> for the hbonds like this :- >> >> std. dev. relative deviation of >> standard --------- cumulants from those of >> set average deviation sqrt(n-1) a Gaussian distribition >> cum. 3 cum. 4 >> SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.181 3.495 >> SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.421 5.001 >> >> When I calculated the average manually, by taking the average of numbers >> in >> second column of hbnum.xvg file, I got a value of around 13.5.. What is >> the >> reason for such a large difference. >> >> > Hard to say, but I've never known g_analyze to be wrong, so I'd suspect > something is amiss in your manual calculation. The difference between 13.5 > and 0.0069 is huge; you should be able to scan through the data file to see > what the expected value should be. > > > In another case, g_analyze gives avg values of aroun 6.9 for hbond between >> two residues and when I calculated it maually I got the avg values as 6.8 >> >>> .. >>> >> >> Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time >> and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond >> analysis ?? >> > > Data sets 1 and 2. You will note that there are two columns of data in > the -hbnum output produced by g_hbond, with titles explaining both. > > -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 > -- 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
