Table 5. Clustering Results from the Combined Trajectories of All Five Tetramers Run Using the Current Amber Force Field (ff10) and the Force Field Derived in This Worka.
| sequence | force field | % noise | cluster no. | % of frames | average distance within cluster (Å) | standard deviation within cluster (Å) | average distance between clusters (Å) | RMSD of centroid to A-form (Å) |
|---|---|---|---|---|---|---|---|---|
| AAAA | ff10 | 32.7 | 1 | 55.9 | 2.67 | 0.72 | 4.49 | 1.89 |
| 2 | 4.2 | 1.08 | 0.38 | 4.02 | 5.27 | |||
| 3 | 2.5 | 0.78 | 0.24 | 3.73 | 5.01 | |||
| 4 | 2 | 1.39 | 0.35 | 4.33 | 4.42 | |||
| this work | 39.7 | 1 | 28.1 | 1.67 | 0.54 | 3.89 | 2.42 | |
| 2 | 9.2 | 2.18 | 0.67 | 3.80 | 3.68 | |||
| 3 | 5.5 | 1.53 | 0.40 | 3.63 | 4.74 | |||
| 4 | 5.4 | 1.68 | 0.43 | 4.16 | 1.33 | |||
| CAAU | ff10 | 13.3 | 1 | 73.3 | 0.97 | 0.48 | 4.57 | 4.60 |
| 2 | 8.8 | 2.00 | 0.53 | 3.26 | 2.65 | |||
| 3 | 3.5 | 1.94 | 0.65 | 3.79 | 1.00 | |||
| 4 | 0.7 | 0.96 | 0.36 | 4.04 | 4.16 | |||
| this work | 19.1 | 1 | 66.0 | 1.43 | 0.52 | 3.04 | 2.52 | |
| 2 | 10.0 | 1.42 | 0.45 | 3.47 | 1.46 | |||
| 3 | 3.6 | 1.06 | 0.36 | 3.39 | 4.56 | |||
| 4 | 1.0 | 0.88 | 0.28 | 3.13 | 4.00 | |||
| CCCC | ff10 | 6.2 | 1 | 72.7 | 1.13 | 0.43 | 3.75 | 4.87 |
| 2 | 11.4 | 1.76 | 0.76 | 4.02 | 1.91 | |||
| 3 | 7.7 | 1.88 | 0.64 | 3.97 | 2.78 | |||
| 4 | 0.8 | 0.99 | 0.42 | 3.81 | 4.40 | |||
| this work | 3.3 | 1 | 93.9 | 1.71 | 0.64 | 4.11 | 2.25 | |
| 2 | 1.6 | 1.25 | 0.42 | 4.96 | 4.76 | |||
| 3 | 1.1 | 0.83 | 0.27 | 5.21 | 4.40 | |||
| GACC | ff10 | 20.0 | 1 | 21.3 | 1.66 | 0.77 | 3.93 | 1.46 |
| 2 | 19.6 | 1.76 | 0.61 | 3.98 | 2.61 | |||
| 3 | 7.7 | 1.34 | 0.48 | 3.85 | 4.83 | |||
| 4 | 6.9 | 1.11 | 0.35 | 5.43 | 5.89 | |||
| this work | 15.0 | 1 | 45.0 | 1.43 | 0.53 | 3.78 | 2.47 | |
| 2 | 28.0 | 1.18 | 0.41 | 3.78 | 1.74 | |||
| 3 | 3.8 | 0.79 | 0.24 | 4.23 | 4.44 | |||
| 4 | 2.6 | 0.92 | 0.30 | 4.38 | 4.75 | |||
| UUUU | ff10 | 28.5 | 1 | 39.8 | 1.52 | 0.61 | 4.41 | 5.64 |
| 2 | 9.9 | 1.27 | 0.40 | 4.43 | 5.79 | |||
| 3 | 8.8 | 2.04 | 0.57 | 4.52 | 2.67 | |||
| 4 | 4.7 | 1.27 | 0.40 | 4.29 | 5.04 | |||
| this work | 18.5 | 1 | 72.8 | 1.43 | 0.60 | 3.06 | 2.78 | |
| 2 | 3.7 | 0.88 | 0.33 | 4.33 | 4.28 | |||
| 3 | 3.3 | 1.41 | 0.43 | 3.23 | 1.53 | |||
| 4 | 1.0 | 1.22 | 0.29 | 3.67 | 3.71 |
a
Only the top 4 clusters are presented. The sizes of the remaining clusters (if they existed) were always less than 5% of total frames in trajectory. Starting from the left, columns denote molecule type, force field used, % of noise frames (those that did not get placed in a cluster), cluster number, % of frames within that cluster, average distance and standard deviation between elements of that cluster, average distance between that and all other clusters, and finally mass-weighted RMSD of the centroid of the cluster to the A-form conformation of the respective molecule.