Table 2. Free Energies for the Decoupling of Oseltamivir from the Neuraminidase Active Site As Calculated with cMD and Selective aMD for Varying Equilibration and Sampling Periods.
| simulation type | equilibration time | sampling time | free energy (kcal/mol) |
|---|---|---|---|
| cMD | 1 ns | 1 ns | 71.0 ± 1.4 |
| 2 ns | 70.5 ± 1.5 | ||
| 3 ns | 69.5 ± 1.6 | ||
| 4 ns | 68.4 ± 1.3 | ||
| 2 ns | 1 ns | 69.6 ± 2.2 | |
| 2 ns | 68.5 ± 2.0 | ||
| 3 ns | 67.6 ± 1.5 | ||
| 3 ns | 1 ns | 66.8 ± 1.8 | |
| 2 ns | 66.9 ± 1.2 | ||
| aMD | 250 ps | 500 ps | 70.5 ± 1.4 |
| 750 ps | 69.4 ± 1.0 | ||
| 1000 ps | 69.2 ± 1.2 | ||
| 1250 ps | 68.7 ± 1.1 | ||
| 500 ps | 500 ps | 69.2 ± 1.2 | |
| 750 ps | 69.0 ± 1.1 | ||
| 1000 ps | 68.3 ± 1.2 | ||
| 750 ps | 500 ps | 67.9 ± 1.4 | |
| 750 ps | 67.3 ± 1.5 |