The computational framework in this study, illustrated in Fig , has three main components. First, the photoisomerization process is modeled with QM surface-hopping MD; second, classical MD at the microsecond timescale is used to study the THI mechanism and obtain quantities related to performance, such as rate constants and free energies. Finally, to achieve realistic classical MD results, we adjust force field parameters against conformational energies from reference QM calculations. The three components are described in the following subsections. Additional details are provided in the Electronic Supplementary Information (ESI); scripts and input files to reproduce this study can be downloaded from a Github repository (github.com/fengmudong/motor-paper).