Table 3. Clustering Analysis of Trajectories from Parallel-Stranded GQ Simulations.

simulation no.	starting structure and conditionsa	loop no.b	no. of clusters obsd	cluster	population (%)	loop no.b	no. of clusters obsd	cluster	population (%)	loop no.b	no. of clusters obsd	cluster	population (%)
1	1KF1 with Na+ in bsc0χOL4	loop 1	5	1	27.8	loop 2	9	1	30.0	loop 3	4	10	18.6
				3	60.6			9	3.4			16	28.9
				16	7.8			4	53.8			1	33.1
				8	3.5			8	1.2			3	19.3
				additional one cluster with sampling <1%				7	5.2
								5	5.4
								additional three clusters with each sampling <1%
2	1KF1 with Na+ in bsc0χOL4εζOL1	loop 1	6	1	23.9	loop 2	11	1	32.8	loop 3	16	1	9.8
				13	2.8			4	14.2			18	21.2
				3	47.4			5	25.8			8	12.6
				2	21.8			10	7.5			2	7.2
				9	3.5			6	5.6			13	1.2
				additional one cluster with <1% sampling				9	9.7			9	13.6
								2	1.4			7	5.8
								15	1.1			16	4.3
								additional three clusters with each sampling <1%				3	15.6
												11	1.8
												10	5.0
												additional five clusters with each sampling < l%
3	1KF1 with K+ in bsc0χOL4	loop 1	10	3	25.6	loop 2	7	1	4.7	loop3	16	15	3.2
				9	2.5			10	6.7			1	9.8
				1	39.1			12	69.3			18	2.1
				10	5.1			16	1			10	12.8
				2	19.3			3	7.4			12	33.7
				18	4.2			19	10.4			6	15.4
				17	2.6			additional one cluster with sampling <1%				4	9.7
				additional three clusters with each sampling <1%								3	4.4
												19	1.9
												20	2.6
												5	1.7
												additional five clusters with each sampling <1%
4	lK8P with Na+ in bsc0χOL4	loop 1	5	1	88.1	loop 2	7	1	45.2
				3	1.8			7	17.0
				4	7.9			4	17.2
				7	2.1			11	9.8
				additional one cluster with <1% sampling				18	5.4
								12	2 2
								19	3.3
5	lK8P with Na+ in bsc0χOL4εζOL1	loop 1	2	1	98.4	loop 2	3	1	14.8
				19	1.6			4	29.3
								8	55.8

^aOnly the stabilizing cations and the force field used for simulations are listed here. See Methods for a detailed description of simulation conditions.

^bThe number of the loop counted from the 5′-end of the GQ.