Hello Erik, I did the same.
Thanks, Nilesh > Hi Nilesh, > > You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the > contacts in the last column of hb.xvg. > > Kind regards, > Erik > >> On 10 Jul 2015, at 15:58, Nilesh Dhumal <ndhu...@andrew.cmu.edu> wrote: >> >> I don't understand why am I not getting hydrogen bond,if I use cufoff >> 0.25nm? >> >> Nilesh >> >>> But without contact you will need a full donor-hydrogen-acceptor triad >>> for >>> it to be registered, which is not what you want as far as I can tell. >>> >>> Erik >>> >>>> On 10 Jul 2015, at 15:17, Nilesh Dhumal <ndhu...@andrew.cmu.edu> >>>> wrote: >>>> >>>> This is index file >>>> >>>> [ O8-H18-1 ] >>>> 8 18 >>>> [ O8-H18-2 ] >>>> 4032 >>>> >>>> >>>> Found 1 donors and 2 acceptors >>>> >>>> Its look contact YES check the distance between accetpr---donor. >>>> >>>> I will run without contact. >>>> >>>> Nilesh >>>> >>>>> Hi Nilesh, >>>>> >>>>> Am not sure it accepts hydrogens as donors/acceptors even with >>>>> -contact. >>>>> How many donors and acceptors are found? >>>>> >>>>> Kind regards, >>>>> Erik >>>>> >>>>>> On 10 Jul 2015, at 14:37, Nilesh Dhumal <ndhu...@andrew.cmu.edu> >>>>>> wrote: >>>>>> >>>>>> I calculated number of hydrogen bond with cutoff 0.25 nm (Distance >>>>>> between >>>>>> hydrogen and O,acceptor) using g_hbond, >>>>>> >>>>>> g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg >>>>>> -nonitacc >>>>>> -r 0.25 -contact -dist >>>>>> >>>>>> The found the calculated number of hydrogen bond along time are zero >>>>>> and >>>>>> -nan is the in hbdist.xvg file. >>>>>> I calculated the distance between hydrogen and oxygen using g_dist >>>>>> and >>>>>> the >>>>>> calculated the distance is less than 0.25 nm. >>>>>> >>>>>> Why am I getting zero number of hydrogen bonds using g_hbond (based >>>>>> on >>>>>> same cutoff )? >>>>>> >>>>>> Nilesh >>>>>> >>>>>> >>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> I will use two groups. >>>>>>> >>>>>>> Nilesh >>>>>>>> >>>>>>>> On 7/9/15 9:13 PM, Nilesh Dhumal wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 7/9/15 9:02 PM, Nilesh Dhumal wrote: >>>>>>>>>>> Hello, >>>>>>>>>>> >>>>>>>>>>> I am calculating g_hbond for water system. I have a question >>>>>>>>>>> about >>>>>>>>>>> specifying two group for calculating hydrogen bond. >>>>>>>>>>> >>>>>>>>>>> Do I specify atoms in triplet(O-H---O)? >>>>>>>>>>> Can I specify O-H as one group (Donor-Hydrogen) and O in other >>>>>>>>>>> group >>>>>>>>>>> (Acceptor)? >>>>>>>>>> >>>>>>>>>> If the system is pure water, you do not need any special index >>>>>>>>>> groups. >>>>>>>>> >>>>>>>>> I have DMSO in the system. I just mentioned water to make it >>>>>>>>> simple. >>>>>>>>> I am interested in O--H---O(DMSO) interactions? >>>>>>>>> >>>>>>>>> How should I specify this? >>>>>>>>> >>>>>>>>> With one triplet O--H---O(DMSO) or two groups one O--H and second >>>>>>>>> O(DMSO) >>>>>>>> >>>>>>>> The latter - just use DMSO and water groups. O can be a donor or >>>>>>>> acceptor, and >>>>>>>> g_hbond intelligently figures out whether or not a given atom is a >>>>>>>> donor >>>>>>>> or >>>>>>>> acceptor (or both). >>>>>>>> >>>>>>>> -Justin >>>>>>>> >>>>>>>>>> >>>>>>>>>>> Default -r cutoff is 0.35nm. Is the distance between >>>>>>>>>>> hydrogen---acceptor >>>>>>>>>>> or distance between donor---acceptor? >>>>>>>>>> >>>>>>>>>> Read the first sentence of the help description. >>>>>>>>>> >>>>>>>>>> -Justin >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> ================================================== >>>>>>>>>> >>>>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>>>>>> >>>>>>>>>> Department of Pharmaceutical Sciences >>>>>>>>>> School of Pharmacy >>>>>>>>>> Health Sciences Facility II, Room 629 >>>>>>>>>> University of Maryland, Baltimore >>>>>>>>>> 20 Penn St. >>>>>>>>>> Baltimore, MD 21201 >>>>>>>>>> >>>>>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>>>>>> >>>>>>>>>> ================================================== >>>>>>>>>> -- >>>>>>>>>> Gromacs Users mailing list >>>>>>>>>> >>>>>>>>>> * Please search the archive at >>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >>>>>>>>>> before >>>>>>>>>> posting! >>>>>>>>>> >>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>>> >>>>>>>>>> * For (un)subscribe requests visit >>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>>>>> or >>>>>>>>>> send >>>>>>>>>> a mail to gmx-users-requ...@gromacs.org. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ================================================== >>>>>>>> >>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>>>> >>>>>>>> Department of Pharmaceutical Sciences >>>>>>>> School of Pharmacy >>>>>>>> Health Sciences Facility II, Room 629 >>>>>>>> University of Maryland, Baltimore >>>>>>>> 20 Penn St. >>>>>>>> Baltimore, MD 21201 >>>>>>>> >>>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>>>> >>>>>>>> ================================================== >>>>>>>> -- >>>>>>>> Gromacs Users mailing list >>>>>>>> >>>>>>>> * Please search the archive at >>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>>> posting! >>>>>>>> >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>> >>>>>>>> * For (un)subscribe requests visit >>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>>> or >>>>>>>> send >>>>>>>> a mail to gmx-users-requ...@gromacs.org. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>> or >>>>>>> send >>>>>>> a mail to gmx-users-requ...@gromacs.org. >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>> or >>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send >>>>> a mail to gmx-users-requ...@gromacs.org. >>>>> >>>> >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send >>> a mail to gmx-users-requ...@gromacs.org. >>> >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.