C_HB(T) = <h(t)h(T+t)>/ <h(t)> S_HB(T) = <h(t)H(T+t)>/<h(t)>
h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Ramachandran G wrote: >> >> Dear gromacs users: >> I like to know whether gromacs will calculate S-type hydrogen >> bond correlation function? >> If it so how it can be done? Thank you. > > What does that mean? > > >> >> Rama >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. _______________________________________________ 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/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/mailing_lists/users.php