Decoding the patterns of ubiquitin recognition from free energy simulations - Supporting information

The free energy profile obtained from the WHAM procedure is a function of the chosen reaction coordinate, with all other degress of freedom integrated out. This implies that these orthogonal degrees of freedom are adequately sampled in each window, which might require much longer timescales than typical window lengths if they feature local minima separated by high free energy barriers. In addition, an individual window trajectory where the system remains in a minimum without visiting any other basins will not show symptoms of insufficient sampling, making the identification of the problem difficult. Zhu and Hummer have proposed that insufficient sampling can be detected by checking the consistency of histograms in neighboring simulation windows: if different states of the orthogonal coordinates are visited in adjacent windows, inconsistent probability distributions of the reaction coordinate will ensue.