Dear Valerio, Have a glance at the paper by Luzar and Chandler.
Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for the integral. Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 29 Aug 2017, at 13:52, Valerio Ferrario <valerio.ferra...@gmail.com<mailto:valerio.ferra...@gmail.com>> wrote: Dear all, I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds with -ac option but resulted in segmentation fault. Therefore from the normal gmx hbond output I used gmx analyze to obtain the autocorrelation function. Therefore, using again gmx analyze with -luzar options and the autorrelated xvg as input I want to calculate the hbonds parameters. I have an output like this: Hydrogen bond thermodynamics at T = 300 K One-way 0.006 156.395 17.174 Integral -0.076 - 13.220 -666.000 Relaxation 1.038 0.963 4.478 So my question is: what are the different values? I do not understand what those values indicate since no "legend" is provide. I guess that 2 of the 3 values for relaxation might be k and k´ (rate constant for breaking and reforming hbonds), but I am not sure... Can anyone help me in interpreting those numbers? -- 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<mailto: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.