pymbar_notebook_examples

Examples illustrating the use of MBAR for various applications in computational and experimental chemistry.

Contents

• 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-analysis
• constant-force-optical-trap/ - calculation of PMF of dsDNA extension from constant-force optical trap experiments
• harmonic-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 data
• umbrella-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.