Examples illustrating the use of MBAR for various applications in computational and experimental chemistry.
alchemical-free-energy/- example illustrating the calculation of free energy differences from simulations with alchemical intermediates between two end states with a number of methods. Note that this example has moved to https://github.com/MobleyLab/alchemical-analysisconstant-force-optical-trap/- calculation of PMF of dsDNA extension from constant-force optical trap experimentsharmonic-oscillators/- examples all of the functionality of pymbar, including validation of the distribution of error estimates.heat-capacity/- calculation of heat capacities using the fluctuation theorem, including Cv at interpolated temperatures.parallel-tempering-2dpmf/- example illustrating computation of 2D PMF from parallel tempering dataumbrella-sampling-pmf/- example illustrating computation of 1D PMF from umbrella sampling data
Currently, only harmonic_oscillators/harmonic-oscillators.ipynb, harmonic_oscillators/harmonic-oscillators-simple.ipynb and umbrella-sampling-pmf/umbrella_sampling.ipynb have been updated as full notebooks rather than conversion of the python scripts.