Fig. 3.

Convergence of the estimate of the folding free energy from VES-RE (A) and PT-WTE (B). We show results from simulations in which all replicas were initiated in the folded state (solid lines) and simulations in which all replicas were initiated in the unfolded state (dashed lines). The horizontal black line indicates the converged result from 100-μs unbiased MD (1). Within 300 ns of simulation time per replica, both of the VES-RE calculations and the result from 100-μs unbiased MD agree with each other within 0.5 kJ/mol, indicating that we can accurately estimate the folding free energy this way regardless of initial conditions. The PT-WTE calculations clearly have not converged in this time scale.