Table 2.
MD simulations
| Trial | Time, ns | Initial structure | Box,* Å | Cutoff,† Å | B′-form,‡ % | B′-form rmsd§ |
|---|---|---|---|---|---|---|
| d(A)10 | ||||||
| A10.0 | 2.0 | B | — | — | 14.3 | 0.096 |
| A10.1 | 10.8 | B | 8 | 8 | 21.8 | 0.076 |
| A10.2 | 8.6 | B | 10 | 8 | 23.4 | 0.071 |
| A10.3 | 8.2 | B | 10 | 12 | 46.2 | 0.069 |
| A10.4 | 1.7 | B | 10 | 15 | 41.8 | 0.067 |
| A10.5 | 6.0 | B′ | 8 | 8 | 13.2 | 0.078 |
| A10.6 | 4.8 | B′ | 10 | 12 | 47.0 | 0.072 |
| d(A)20 | ||||||
| A20.1 | 6.7 | B | 8 | 8 | 19.5 | 0.092 |
| A20.2 | 4.8 | B | 10 | 12 | 49.6 | 0.071 |
| d(AT)10 | ||||||
| AT10.1 | 6.7 | B | 8 | 8 | 5.2 | — |
| AT10.2 | 2.8 | B | 10 | 12 | 9.1 | — |
Explicit water (TIP3P model) was used in all simulations except A10.0, where a generalized Born model was used. Structural parameters tabulated for the MD simulations are listed in Tables 3 and 4, which are published as supporting information on the PNAS web site.
*Minimum distances between DNA and solvent box perimeter.
†Limits for nonbonded interactions.
‡Percentage of the ensemble having B′-form conformations, defined as having the same number of resolved SXD peaks as the experimental d(A)20 SXD pattern.
§The variance between the B′-form MD ensemble subset SXD peak positions and d(A)20 experiment (3°C).