Summary of simulations.

The “Structure” column lists the type of neuraminidase, associated mutations, and drug modeled in each system. The “Atoms” and “Water” columns show total number of atoms, and number of water molecules, respectively. The “Ensemble” column lists the variables held constant during simulations; N, p, T, and V correspond to number of atoms, pressure, temperature, and volume, respectively. Under “Type”, EQ denotes equilibration, and SCV denotes constant velocity SMD simulation with a velocity of 0.05, 0.10, and 0.25 Å/ps, for simSMD1, simSMD2, and simSMD3, respectively. For simEQ1 to simEQ6, the simulation times involve a 20 ns setup/equilibration run followed by a 20 ns production run. SimSMD1 is a steered MD simulation with the starting structure from equilibrated simEQ1 (“locked” drug position). In simFEQ1 to simFEQ10, the starting structure is a bound, rotated position of oseltamivir from simSMD1 after 7.5ns of simulation, when several of the drug's stabilizing hydrogen bonds to the protein are ruptured.