Hi Chris, The activation energy is obtained from the PMF well depth. So that leaves two variables k and A. If we get K at say 5 temepratures, and plot ln(k) vs. 1/T, the intercept will give us A. From that, at the temperature of interest, we can back out k.
I will dig up the paper I saw this in. It was a really long time ago though. On Sun, Oct 6, 2013 at 2:33 AM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > Dear Rajat: > > I just checked the first two papers that you mentioned and they both get > kinetics from standard equilibrium simulations. As for the Arrhenius law, > with k, A, and the energy of activation (Ea) all unknown for each T, how do > you obtain a unique solution for k given T ? Even if you assume that Ea is > some function of the maximum of your PMF (which is not always true), I > presume that you can only then get the relationship between k and A, not > the absolute value of k, even with information from many temperatures. > However, I've never worked on this directly. Can you provide a reference so > that I can take a look? > > Thank you, > Chris. > > -- original message -- > > 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.neale at 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
