On Fri, Oct 07, 2022, Liao via AMBER wrote:
>
>From what I imagine, to judge phase-space overlap, shouldn't one run
>independent simulations of both the starting state and final state, and see
>if their spatial occupancies, after reaching equilibrium state, overlap?
This sounds correct to me, but defining "spatial occupancies" can be hard
in systems with many degrees of freedom. That is why potential energy (a
single variable) gains so much attention.
Note that thermodynamic integration (TI), which is the main tool in Amber for
free energies, doesn't depend in any direct way on phase-space overlap. The
key point for TI is the smoothness of the behavior of <DV/Dlambda> as a
function of lambda.
....dac
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Received on Tue Oct 11 2022 - 09:00:03 PDT
