Molecular dynamics (MD) simulation is a widely-used computational technique to provide atomic-resolution details about the behavior of biomolecular systems. By utilizing a classical approximation of the forces between atoms of the system, a molecular trajectory may be propagated forward in time, showing likely conformational motions and both intramolecular and intermolecular interactions. When the trajectory is written, MD simulations generate large quantities of data, encapsulating the details of the atomic motions. A detailed explanation of generalized correlation within the context of MD is provided below in the Theory section. We repeat and regenerate the results of a seminal GC analysis of the B1 domain of protein G. We also perform a new study on the inter-and intra-molecular correlations within the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump as an additional use case. We also implement a "local alignment" procedure that seems to greatly reduce spurious correlations detected in large or highly flexible structures.