Table 1. Summary of Molecular Dynamics Simulations.
| method | starting structure | number of trajectories | length of simulation | comments |
|---|---|---|---|---|
| AAMD | 1SU4 | 4 | 400 ns | Includes transition trajectory 1SU4* |
| 1WPG | 3 | 400 ns | ||
| 2ZBD | 3 | 400 ns | ||
| AAMD | WT | 6 | 40 ns | Repeated simulations starting from H-bonded intermediate of transition trajectory 1SU4* |
| AAA | 6 | 40 ns | ||
| CGMD | 1SU4 | 1 | 4 μs | |
| 1WPG | 1 | 4 μs | ||
| 2ZBD | 1 | 4 μs | ||
| CGMD | Intermediate structures derived from the open crystal structure 1SU4. | 11 | 1 μs | The distance between the centers of mass of the N and A-domains was harmonically constrained to designated distances between 40 to 30 Å. |