TABLE 1.
Summary of simulations performed
| Simulation number | System simulated | Salt concentration (mM) | Force field/MD integrator | Results (helix-E conformation) |
|---|---|---|---|---|
| 1 | Free pol X, structure A (initially closed) | 150 | CHARMM/LN | Opening trend |
| 2 | Free pol X, structure B (initially open) | 150 | CHARMM/LN | Remains open |
| 3 | Free pol X, structure A (initially closed) | 500 | CHARMM/LN | Remains closed |
| 4 | Free pol X, structure B (initially open) | 500 | CHARMM/LN | Closing trend |
| 5 | Pol X/DNA | 500 | CHARMM/PME | Remains open |
| 6 | Pol X/DNA | 150 | CHARMM/LN | Remains open |
| 7 | Pol X/DNA/dCTP | 150 | CHARMM/LN | Closing trend |
| 8 | Pol X/DNA/dCTP | 150 | CHARMM/PME | Closing trend |
| 9 | Pol X/DNA/dCTP | 150 | CHARMM/LN/different initial velocity | Closing trend |