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List of Figures

  1. Graph of van der Waals potential with and without switching
  2. Graph of electrostatic potential with and without shifting function
  3. Graph of electrostatic split between short and long range forces
  4. Example of cutoff and pairlist distance uses
  5. Convergence of an FEP calculation. If the ensembles representative of states $a$ and $b$ are too disparate, equation (8) will not converge (a). If, in sharp contrast, the configurations of state $b$ form a subset of the ensemble of configurations characteristic of state $a$, 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 $a$ to $b$ (c). It should be mentioned that in practice, the kinetic contribution, ${\cal T}({\bf p}_x)$, is assumed to be identical for state $a$ and state $b$.
  6. 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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