On Wed, Jul 04, 2018, emanuele wrote:
>
> I want to use the thermodynamic integration method to calculate the free
> energy of a reaction A + e- → A- , and then get the redox potential from
> the free energy. Now I would know how many calculations I should run for
> this simply reaction, and in addition how to post-process the outputs?
Redox potential calculations are just an analogue of pKa calculations, adding
an electron rather than a proton. Take a look at the tutorial on "pkA
calculations using thermodynamic integration" for a start.
(Note also that we now support "constant redox potential" simulations that are
analgous to "constant pH" simulations. Depending on your needs, this can
sometimes be a useful alternative to TI.)
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 04 2018 - 06:00:07 PDT
