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- Graph of van der Waals potential with and without switching
- Graph of electrostatic potential with and without shifting function
- Graph of electrostatic split between short and long range forces
- Example of cutoff and pairlist distance uses
- Convergence of an FEP calculation. If the ensembles representative
of states
and
are too disparate, equation (8) will
not converge (a).
If, in sharp contrast, the configurations of
state
form a subset of the ensemble of configurations
characteristic of state
, the simulation is expected
to converge (b).
The difficulties reflected in case (a) may be
alleviated by the introduction of mutually overlapping intermediate
states that connect
to
(c). It should be
mentioned that in practice, the kinetic contribution,
,
is assumed to be identical for state
and state
.
- Dual topology description for an alchemical simulation.
Case example of the mutation of alanine into serine.
The lighter color denotes the non-interacting, alternate
state.
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