Table 5. Time It Took for Non-A-Form Starting Structures To Reach a Structure in Reasonable Agreement with NMR Spectra.

starting structure	force field	time segment of simulation used for analysis of MD (ns)a	no. of major transitions observed
C3′-endo/anti	parm99	0–1500b	many
	parm99χ_YIL	0–1500b	0
	parm99TOR	0–770b,d	2
C3′-endo/syn	parm99	–c	many
	parm99χ_YIL	65–597e	3
	parm99TOR	290–1500	2
C2′-endo/anti	parm99	–c	many
	parm99χ_YIL	35–1500	3
	parm99TOR	1093–1500	2
C2′-endo/syn	parm99	–c	many
	parm99χ_YIL	22–1500	2
	parm99TOR	991–1500	2

^aThe time period evaluated for MD simulations was chosen from the point at which simulations show reasonable agreement with the NMR distances and expected torsion angles until a structure inconsistent with NMR data is observed or the simulation reaches its end. Reasonable agreement with the NMR distances and expected torsion angles is defined as 60% agreement with the 27 NOEs within error limits (Table 4), three β dihedrals (between 150° and 210°), and four γ dihedrals (between 40° and 80°).

^bSimulations started as A-form and were evaluated for the entire simulation unless otherwise noted.

^cSimulations did not show reasonable agreement with the NMR distances and expected torsion angles, so these trajectories were not evaluated.

^dOnly the first 770 ns was used because after 770 ns, C1 intercalated between C3 and C4.

^eAfter 597 ns, C1 intercalated between C3 and C4.