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pymbar-examples

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Examples of applications of pymbar to various problems in simulation and experiment

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pymbar-examples
===============

NOTE: THESE EXAMPLES HAVE BEEN MOVED TO THE MAIN PYMBAR REPOSITORY.  FUTURE DEVELOPMENT WILL HAPPEN THERE.

Examples illustrating the use of [MBAR](http://github.com/choderalab/pymbar) 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

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