Targeting PDE6D for inhibiting KRAS: A computational approach Furthermore, the simulation interaction diagram module of the Desmond program was used to conduct more research on the root means square deviation (RMSD), root means square fluctuation (RMSF), ligand torsion, and protein-ligand interactions profiling (Maestro). Thus, the trajectory's root means square deviation (RMSD) was determined for each frame. The equation for RMSD for frame x was as represented below: