Recurrence quantification analysis as a tool for the characterization of   molecular dynamics simulations
  A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG) simulated in water are analyzed by recurrence quantification, which is noteworthy for its independence from stationarity constraints, as well as its ability to detect transients, and both linear and nonlinear state changes. The results demonstrate the sensitivity of the technique for the discrimination of phase sensitive dynamics. Physical interpretation of the recurrence measures is also discussed. 
Cesare Manetti, Marc-Antoine Ceruso, Alessandro Giuliani, Charles L.   Webber, Jr. and Joseph P. Zbilut