Hi Chris, I have never done this and I may be missing something. But here is what I think. I have seen a few papers use the Arrhenius law, k=A*exp (-deltaG/kB*T)...-deltaG/kB*T can be obtained from the PMF...Now, if you do this for different temperatures, you can back out the activation energy and hence the rate constant. I would love to learn more about this. Any inputs will be welcome.
Regards, On Sat, Oct 5, 2013 at 11:44 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > If you want K_on and K_off, then I think you need to look at long-time > equilibrium simulations or massively repeated simulations connected with a > MSM. Beyond that, I believe that you will need to understand all of the > important free energy barriers in all degrees of freedom (hard, to say the > least). > > Rajat: how are you going to compute kinetics from a PMF? Barriers in > orthogonal degrees of freedom don't show up on your PMF but can greatly > affect the kinetics. Even relatively minor roughness of the > multidimensional free energy surface and off-pathway kinetic traps are > going to affect the kinetics but not the PMF. Some people have tried to > circumvent this limitation by using the PMF in addition to computing the > local diffusion at each small section of the order parameter (e.g., > http://www.nature.com/nnano/journal/v3/n6/full/nnano.2008.130.html ) but > unless there is excellent sampling overlap and lots of transitions between > all relevant states, I see this as a way to calculate an upper bound of > rates that I think could easily be much slower. See, for example, > http://pubs.acs.org/doi/abs/10.1021/jp045544s . Finally, I am not sure > how rates can be usefully extracted from a non-equilibrium method like REMD. > > Unless I missed it, the paper that David cites: > http://pubs.acs.org/doi/abs/10.1021/ct400404q doesn't compute kinetics. > > Perhaps the OP can provide more information on what they are trying to > obtain, exactly. > > Chris. > > -- original message -- > > 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. > > -- > 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 > -- 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
