Sketch of SMD simulation and the umbrella sampling method. (a) In SMD simulation, one terminus of the protein of interest is fixed, while the other terminus is coupled with a dummy spring with linear elastic constant k. The other end of the spring moves away from the protein with constant velocity v to stretch the protein. (b) In umbrella sampling, in conformational space projected to the extension as the reaction coordinate, the folded state and the unfolded state are located at each end of the coordinate. Between the folded state and the unfolded state, a spring is used to restrain conformations in a small window of conformational space. The system is well sampled in each window, and overlapping between neighboring windows helps to build PMF of the protein.