Table 2:
Summary of the efficiency of each technique (in force evaluations) in each system (PDBid listed) simulation. All ordered water molecules were removed prior to simulations. If any simulation failed to rehydrate each target site based on our defined criteria, the result is shown as ”F” in the table. We calculated force evaluations (in million evaluations) required to achieve the point where all hydration sites were successfully rehydrated in each simulation. The calculated force evaluations include both equilibration and production phases. See Section 3 for detailed force evaluation in equilibration phases for each method. ”N.D.” means no data since the simulation was not conducted.
| 2QBS | 2XAB | 2XJG | 3RLP* | 3RLQ | 3RLR | 5I29* | 4ZLZ* | 5I1Q* | 2ZFF* | |
|---|---|---|---|---|---|---|---|---|---|---|
| BLUES (restrained) | 8.3/13.9/6.9 | 23.5/41.5/23.5 | 6.9/6.9 | 113.5/167.5 | 41.5/23.5/23.5 | 6.9/23.5 | 6.9/6.9 | 6.9/8.3 | 12.5/13.9 | F/F |
| MD (unrestrained) | 40.5/F | F/F | 145.5/F | F/35 | F/F | F/F | 12.5/18.1 | 6.9/13.9 | F/F | 40.5/11.1 |
| MD (restrained) | F/F | F/F | F/F | F/F | F/F | F/F | 6.9/6.9 | F/F F/F | F/F | F/F |
| grand (unrestrained) | F/2.1 | 0.7/2.1 | 0.7/0.7 | 3.5/3.5 | 0.7/0.7 | 0.7/0.7 | 2.1/2.1 | 2.1/2.1 | 9.1/F | 2.1/2.1 |
| grand (restrained) | 0.7/0.7/0.7 | N.D. | N.D. | N.D. | N.D. | N.D. | N.D. | N.D. | N.D. | F/F/F |
*
based on the electron density map analysis.