NOTE: THESE EXAMPLES HAVE BEEN MOVED TO THE MAIN PYMBAR REPOSITORY. FUTURE DEVELOPMENT WILL HAPPEN THERE.
Examples illustrating the use of MBAR for various applications in computational and experimental chemistry.
alchemical-free-energy/- example illustrating calculation of free energy difference from simulations of alchemical intermediatesconstant-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