pymbar-examples

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

Contents

• alchemical-free-energy/ - example illustrating calculation of free energy difference from simulations of alchemical intermediates
• 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