. Author manuscript; available in PMC: 2018 Oct 3.

Published in final edited form as: J Chem Theory Comput. 2016 Aug 4;12(9):4534–4548. doi: 10.1021/acs.jctc.6b00300

Table 1.

List of all simulations of 8-mer GAGA TL with sequence 5’-gcGAGAgc-3’ and 10-mer GAGA TL with sequence 5’-cgcGAGAgcg-3’. χ_OL3-neut.-fold and χ_OL3-neut.MetaD simulations started from the folded state, while all others were initiated from the unfolded state.

System	Method	Ionic conditions	Force field	Label	Length
8-mer	T-REMD	1M KCl	χ_OL3	χ_OL3-1M	1 μs x 64
			χ_OL3+HBfix 1 kcal	χ_OL3HB-1M	2 μs x 64
			χ_OL3+HBfix 0.5 kcal	χ_OL3HB_0.5-1M	1 μs x 64
			ff99Chen	ff99Chen	2 μs x 64
			χ_OL3-CP	χ_OL3CP-1M	2 μs x 64
			χ_OL3-CP+HBfix 1 kcal	χ_OL3CP-HB-1M	2 μs x 64
		K⁺ net-neutral	χ_OL3	χ_OL3-neut.	1 μs x 64
		K⁺ net-neutral	χ_OL3	χ_OL3-neut.-fold	2 μs x 64
	REST2	1M KCl	χ_OL3	χ_OL3-1M-REST	1 μs x 64
10-mer	T-REMD	K⁺ net-neutral	χ_OL3	χ_OL3-neut.-10mer	1 μs x 64
10-mer	WT-MetaD	Na⁺ net-neutral	χ_OL3	χ_OL3-neut.MetaD	3 μs x 2