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README.md

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README.md

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pymbar-examples

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

Contents

  • umbrella-sampling-pmf/ - example illustrating computation of 1D PMF from umbrella sampling data
  • alchemical-free-energy/ - example illustrating calculation of free energy difference from simulations of alchemical intermediates
  • parallel-tempering-2dpmf/ - example illustrating computation of 2D PMF from parallel tempering data
  • constant-force-optical-trap/ - calculation of PMF of dsDNA extension from constant-force optical trap experiments
  • heat-capacity/ - calculation of heat capacities using the fluctuation theorem, including Cv at interpolated temperatures.