English: Filtered Random Motion Removal for Example SMX Containing Trajectory. Filtered trajectory for simulation shown in movie 1. Filtered trajectories use averaging of motion with N=3 using the Gromacs filter (cosine(π*time frames/N) to remove random movements caused by oscillation or random solvent effects. Resultant motions are non-random and associated with overall domain changes in the TCR as it moves from pHLA bound to free in solvent across the simulation. These motions are also observed from PCA analysis and simple RMSD or RMSF analysis in static representations. Trajectory 5 was used to produce movie.