Fig. 6
From: JEDi: java essential dynamics inspector — a molecular trajectory analysis toolkit
Correlation analysis shown with increasing sparsification threshold. a, c, and e shows the top two squared modes from each analysis with thresholds of 0.0, 0.5, 0.7 respectively showing how the information encoded in each mode becomes more localized with increasing sparsification. b, d, and f show the total root mean square fluctuations (RMSF) of the subset captured by the top ten modes from PCA. These indicate that while modes become more localized, the total information in the essential subspace is roughly conserved. Finally, g) shows the RMSIP for the sparsified analyses compared to the un-sparsified analysis