On Fri, Dec 20, 2013, zhongqiao hu wrote:
>
> Thank you very much for your reply. I used Amber12 to do umbrella sampling
> to get PMF. I want to decompose it into electrostatic and van der Waals
> contributions. it is something like decomposition into enthalpic and
> entropic contributions.
Unlike entropy and enthalpy, there is no unique decomposition of PMF's into
"parts", and this has nothing do with whether or not the potential is pairwise
additive or not.
You could compute a PMF with all charges set to zero, and call that the "vdW
contribution". Then the difference between that and the full PMF could be
called the "electrostatic contribution". But these defintions are
arbitrary; whether they offer much insight must depend on the detailed
situation.
Note that decomposing a PMF is rather different than trying to decompose
an alchemical or binding free energy change. For the latter, there are
arbitrary but often rather reasonable and helpful ways to decompose the
contributions into parts.
....dac
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Received on Fri Dec 20 2013 - 07:00:02 PST
