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.