Hi, If you are looking at binding/unbinding as a function of temperature (hopefully with REMD), you can use g_kinetics. If you are looking at unbinding/binding events in a single simulation with temperature, etc constant (no annealing), you will need to calculate binding probabilities, from which you can back out a rate constant. A simple google search gave me these papers (http://www.pnas.org/content/90/20/9547.full.pdf, http://pubs.acs.org/doi/abs/10.1021/jp037422q)
Of course, the best approach is to calculate the PMF and back out the rate constant from the free energy. Hope that helps. On Fri, Oct 4, 2013 at 4:00 PM, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I've submit a simulation in gromacs, and I am just wondering how can we > calculate kinetic constant for the ligand bound/ubound process? > > thanks a lot > Albert > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
