Table 1. List of the Simulations Carried out in the Present Study.

quadruplex topology	loop sequence	PDB id	ion conditions	force field	length of the simulation	simulation reference number used in the text
intramolecular parallel-stranded DNA GQ	propeller-propeller-propeller	1KF1	excess 0.15 M NaCl	bsc0χOL4	10 μs	1
			excess 0.15 M NaCl	bsc0χOL4εζOL1	10 μs	2
			excess 0.15 M KCl	bsc0χOL4	10 μs	3
bimolecular parallel-stranded DNA GQ	propeller	1K8P	excess 0.15 M NaCl	bsc0χOL4	10 μs	4
	propeller		excess 0.15 M NaCl	bsc0χOL4εζOL1	4 μs	5
(3+1) hybrid-1 DNA GQ	propeller-lateral-lateral	2HY9	excess 0.15 M NaCl	bsc0χOL4	10 μs	6
			excess 0.15 M NaCl	bsc0χOL4εζOL1	10 μs	7
		2GKU	excess 0.15 M NaCl	bsc0χOL4εζOL1	10 μs	8
(3+1) hybrid-2 DNA GQ	lateral–lateral-propeller	2JPZ	excess 0.15 M NaCl	bsc0χOL4	10 μs	9
			excess 0.15 M NaCl	bsc0χOL4εζOL1	10 μs	10
antiparallel (2+2) DNA GQ	lateral-propeller-lateral	2MBJ	excess 0.15 M NaCl	bsc0χOL4	10 μs	11
			excess 0.15 M NaCl	bsc0χOL4εζOL1	10 μs	12
intramolecular parallel-stranded DNA GQ	propeller-propeller-propeller	1KF1	excess 0.15 M NaCl	bsc0χOL4εζOL1 and restraints on γ-dihedral (γ ∼ 180°) of the first thymine of all three propeller loops	3.4 μs	13
			excess 0.15 M NaCl	bsc1	2 * 1 μs	14, 15
			excess 0.15 M NaCl	OL15	10 μs	16
			excess 0.15 M NaCl and OPC waters	OL15	10 μs	17
			excess 0.15 M KCl and OPC waters	OL15	10 μs	18