Table 2. Summary of the results from the cluster analysis of the simulations of wild-type munc18a and munc18aS306D,S313D (dt = 10 ps).
| Condition | Number of clusters | Number of clusters≥1% of ∑structures | % of largest three clusters out of ∑structures | # Cluster | Munc18a (1) mean distance | Munc18aS306D, S313D (M1) mean distance |
| Munc18a WT (n = 3) | 72 (3) | 34 (3) | 16.3 (3) | 1 | 3.8 (0.1) | 3.52 (0.05) |
| Munc18aS306D,S313D (n = 2) | 48 (5) | 25 (1) | 27.15 (3) | 2 | 3.7 (0.06) | 3.48 (0.06) |
| 3 | 3.9 (0.1) | 3.39 (0.06) |
Cluster analysis segments the structures that the protein samples during the simulation into sub-groups according to an adjustable RMSD cut-off value that reflects the extent of similarity between the structures. The analysis was performed using the Gromos algorithm (RMSD cut-off of 0.2 nm). The table presents the average total number of clusters, the number of clusters that comprise more than 1% of the total number of structures, the percentage of the three main clusters out of the total number of clusters, and the mean distance between the centers of mass of domains 3a and 1 together with the STDEV in the three largest clusters of simulations 1 and M1.