Table 1. Outcome of all 48 simulations (200 ns each) of the antiparallel d[AGGGTTAGGG] hairpin with the bsc0χ_OL4ϵζ_OL1 force field.

Groove width	s/a pattern				Water and ionic parametersa
	5′-asa–-sas-3′	5′-saa–-ssa-3′	5′-ssa–-saa-3′	5′-sas—asa-3′
Narrow	3 O	1,2,3 tW*	3O*;1,2,3 tW*	P: 1 O	TIP3P	NaCl	J&C
	3 O*	2 tW		3 tW*	TIP3P	KCl	J&C
	3 O*	2 tW			TIP3P	NaCl	Aq.
	3 O*			U: S5	SPC/E	NaCl	J&C
	3 O				SPC/E	KCl	Aq.
		P: 1,2,3 tW	2,3 tW*	U: 1,2,3 O	SPC/E	KCl	Dang
Wide	U: S5	U: S5	U: 1,2,3 O*; S5	U: 1,2,3 O	TIP3P	NaCl	J&C
	P: S5	1,2,3 tW	U: 1,2,3 O	P: 2,3 O*	TIP3P	KCl	J&C
	3 O	U: 1,2,3 tW	See text	U: 2,3 tW*; 1,2,3 O	TIP3P	NaCl	Aq.
	U: S5	P: 1,2,3 tW	U: 1,2,3 O		SPC/E	NaCl	J&C
			U: 1,2,3 O	U: 1,2,3 O	SPC/E	KCl	Aq.
	U: 2,3 O; 1 tW		P: 1 O; 2,3 tW	P: G; 1 O	SPC/E	KCl	Dang

Final structures in the 12 × 4 matrix are classified in the following way: no text or regular font text mean that the final structure resembles the starting structure with at least two native cWH GG pairs at the end of the simulation (loss of one base pair is tolerated). ‘P:’ stands for any other hairpin-like structure at the end (perturbed structures, see the text). ‘U:’ means entire disruption of the hairpin, e.g. unwinding to ss-helix or coil formation. Characteristic structural rearrangements in the simulations are described by the following symbols: ‘O’ means opening (loss) of a particular GG pair (1–closing the loop, 2–middle, 3–terminal pair), ‘tW’ means transition of the GG pair from cWH to tWW geometry, ‘S5’ and ‘S3’ mean strand slippage towards the 5′- or 3′-terminus with base pairing shifted by one base (Figure 3 depicts example of a structure with S5 slippage), ‘G’ means conversion from initial narrow groove to wide groove or vice versa (see Figure 2). ‘*’ denotes that the particular rearrangement was reversible and the initial cWH pairing was restored. Rearrangements shown for the unstable (U:) trajectories are always temporary, i.e. we mark those seen before the entire loss of the structure. If more structural changes occurred, they are divided by ‘;’ and ordered chronologically.

^aJ&C: TIP3P-adapted or SPC/E-adapted Joung & Cheatham parameters; Aq: Amber-adapted Aquist Na⁺ with Dang & Smith Cl^- parameters; Dang: Dang K⁺ with Dang & Smith Cl^- paremeters.