[gmx-users] how to calculate kinetic constant?

[rajat desikan]

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.
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore