Re: [AMBER] TI calculations

From: David A Case <>
Date: Wed, 4 Jul 2018 08:47:19 -0400

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.)


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Received on Wed Jul 04 2018 - 06:00:07 PDT
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