Table 1.
Simulation details for CGMD using MARTINI models of wild type, Delta, and Omicron.
| Simulation settings | Wild type | Delta | Omicron |
|---|---|---|---|
| Density (initial setting before NPT) | 1.00 g/cm2 | 1.00 g/cm2 | 1.00 g/cm2 |
| Simulation box (lx* ly* lz) | 189.7 Å* 158.21 Å* 247.77 Å | 181.80 Å* 159.03 Å* 242.96 Å | 173.91 Å* 159.86 Å* 238.15 Å |
| Dielectric constant | 2.5 | 2.5 | 2.5 |
| Time step size | 10.0 fs | 10.0 fs | 10.0 fs |
| Temperature | 310 K | 310 K | 310 K |
| Pressure | 1 atm | 1 atm | 1 atm |
| Spike protein | 2499 beads | 2496 beads | 2491 beads |
| ACE2 | 1375 beads | 1375 beads | 1375 beads |
| Polarized water beads | 185549 beads | 135086 beads | 164414 beads |
| Cation (Qd type) | 26 beads | 27 beads | 27 beads |