File:Hamiltonian-exchange-reduced-potential.png
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Reduced potential as a function of iteration for Hamiltonian exchange simulation, computed as
- [math]\displaystyle{ u(X_t) = \sum_{k=1}^K u_{s_{kt}}(x_{kt}) }[/math]
where [math]\displaystyle{ u_i(x) }[/math] is the reduced potential for thermodynamic state index [math]\displaystyle{ i }[/math] and [math]\displaystyle{ s_{kt} }[/math] is the thermodynamic state index for replica [math]\displaystyle{ k }[/math] at iteration [math]\displaystyle{ k }[/math].
This example comes from a Hamiltonian exchange implicit solvent alchemical free energy calculation of p-xylene binding to T4 lysozyme L99A.
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| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 15:44, 22 December 2013 | | 1,205 × 378 (51 KB) | John Chodera (talk | contribs) | Reduced potential as a function of iteration for Hamiltonian exchange simulation, computed as : <math> u(X_t) = \sum_{k=1}^K u_{s_{kt}}(x_{kt}) </math> where <math>u_i(x)</math> is the reduced potential for thermodynamic state index <math>i</math> and ... |
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