Significant prior work has demonstrated the sensitivity of TODGA self-assembly in n-dodecane to the presence and absence of polar solutes. In the presence of 0. The computational workflow (Figure ) developed in this work sets a standard for future analysis of solution dynamics using the MSM approach, as this has not been extensively performed previously. In the first step of the workflow, the Pol and NonPol system trajectories were separated using the trjconv module of gromacs 43 into a pool of 60 trajectories per system, each representing the time evolution of individual TODGA molecules. Each of the "molecular" TODGA trajectories were then aligned with a reference structure (the first frame of the first TODGA molecule) to remove rotational and translational motion (using the C, N, and O atoms of the polar head group). Splitting the overall simulation trajectory into individual molecular trajectories provides two major advantages for MSM analysis: