Hi, Could you please clarify if the hbond existed in frames for which g_sdangle reported a ADH-angle above 30 deg?
Also, bear in mind that the -merge flag is on by default, so another hydrogen may bridge the donor-acceptor gap. Erik On 24 Apr 2013, at 21:09, kim2811 <kmani...@iastate.edu> wrote: > Hi, is there any other criteria in determining a hydrogen bond? i know that > in order for a bond to exist, donor-acceptor distance should be less than > or equal 3.5A and A-D-H angle less than or equal 30deg. I used g_sgangle to > measure the angle A-D-H of two hydrogen bonds identified when I determined > the hydrogen bonds using g_hbond. What I did is, I separated A-D and H-D as > two groups (i made the atom indices in the order A-D and H-D in the index > file) and measured the angle between these two vectors. However, the A-D-H > angle as a function of time fall above the cut-off of 30deg and I wonder > why. is there any other explanation for this? > > thank you. > > -- > Kristine > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/any-other-criteria-for-h-bond-tp5007623.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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
