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Summary of AAMD simulations.
| Simulation | Non-equillibrium Sampling Methods | GFLOPs/step | Total sampling (μs) |
|---|---|---|---|
| Equilibration (pre-unwinding) | None | 24.9 | 2.107 |
| RNA unwinding | Extrabonds, Distance colvar, MDFF grid | 25.9 | 0.004 |
| RNA post-unwinding | Atom restraint, MDFF | 11.04 | 1.904 |
| RNA post-unwinding | None | 11.04 | 3.916 |
