As can be seen in SI Figure , fast transitions (200 ps) can be long enough to allow for the side chain to reorient, however, the rotamer populations do not resemble those after the transition as observed in a long end state simulation. This does not mean that resulting values are necessarily wrong as they would be if the dominant rotamer were never sampled in the non-equilibrium switches (Sec. 5.3). Here, running shorter transitions, where we sampled the rotamer switching only sometimes, resulted in free energy estimates that were statistically equivalent to those obtained using longer transitions, in which the dominant rotamer was sampled most of the time, presumably because the free energy estimator gives the most weight to those transitions which discover the favorable rotamer. The standard deviation was also comparable among different NEQ protocols (Figure ). This shows that sampling the side chain reorientation in some switching transitions is sufficient. The standard deviation between independent replicates for pose I is higher with the NEQ approach than with the EQ approach for all transitions lengths (0.2-0.3 kcal/mol vs. 0.1 kcal/mol), suggesting that the protein undergoes additional conformational changes.