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
