On Thu, Jan 19, 2012, Sai Kumar Ramadugu wrote:
> One of the papers that I have come across is title "Accurate Estimates of
> Free Energy Changes in Charge Mutations", JCTC, 6, 1884.
>
> The authors suggest that when charged species are mutated, due to the Ewald
> treatment of electrostatics, there is a self-energy term that appears and
> one has to account for it and they suggested a method to do dual mutations.
The Amber PME scheme (and that in other programs) automatically takes into
account the self-energy terms, so it is perfectly OK to do TI calculations
where the total charge changes. Of course, when you finally construct a real
thermodynamic cycle from your results, the total charge will be conserved, but
it is not necessary to make each step conserve charge. This then simplifies
a lot of the TI setup.
...dac
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Received on Thu Jan 19 2012 - 13:00:02 PST
