…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler model for whatever reason.
Erik On 17 Jun 2013, at 13:22, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Hi, > > Yes, the forward and backward rate constants are for hydrogen-bond breaking > and reforming. You seem to have too poor statistics to draw conclusions about > the backward rate, however. You probably need to simulate longer. > > Erik > > On 15 Jun 2013, at 00:38, learnmd <joinforfun8...@gmail.com> wrote: > >> Hi, >> >> I have run a 5 ns simulation with a small protein in water [SPCE]. I am >> interested in the rate of breakage (sense of how quickly / slowly hbonds are >> broken and formed) of hbonds between protein and solvent. I ran g_hbond -ac >> for the trajectory and received the following output: >> >> Normalization for c(t) = 0.0204961 for gh(t) = 4.55478e-07 >> Hydrogen bond thermodynamics at T = 298.15 K >> Fitting parameters chi^2 = 0.0335188 >> Q = 0 >> -------------------------------------------------- >> Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 >> Forward 0.022 46.303 14.035 0.0335188 >> Backward -0.080 -12.447 -666.000 >> One-way 0.068 14.603 11.175 >> Integral 0.020 48.944 14.173 >> Relaxation 0.052 19.211 11.854 >> >> My question is that the 46 ps that is shown for "forward" can be interpreted >> in the sense that I have described above? Or am I missing the point, >> completely. I am grateful for any pointers. >> >> Thanks >> >> >> >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/autocorrelation-output-g-hbond-tp5009171.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 -- 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
