MBAR (Multistate Bennett acceptance ratio)

mbar(u_kl; tol=1e-8, iterations_self=10) -> F

Estimates the free energy differences between different thermodynamnic states by using the Multistate Bennet Acceptance Ratio Method (MBAR). Let K be # of thermodynamic states. u_kl is a K x K Array whose elements are reduced bias-factors or potential energies of state k evaluated at state l. Solvs the MBAR equations by applying self-consistent iterations iterations_self times, followed by the Newton-Raphson iterations. The iteration stops when the difference from the previous falls below the threshold tol.

Returns dimensionless free energies f_k whose elements corresponds to thermodynamics state k.

Example

see Juypter notebooks in MDToolbox.jl/examples/

References

M. R. Shirts and J. D. Chodera, J. Chem. Phys. 129, 124105 (2008).