To compute free energy of folding as a function of temperature, given replica energy time series, replica trajectories, and corresponding native contact fractions, each frame in the trajectory is first classified as folded or unfolded. In general, classification criteria for n conformational states can be used in cg_openmm. Next, MBAR is used to compute the probability expectations P i at each temperature that a structure will be in each conformational state. The free energy change upon folding ∆G ij (T ), or generally upon any conformational state transition, can then be computed from the following relation: