[gmx-users] how to calculate kinetic constant?

[rajat desikan]

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 <mailmd2011 at 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
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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