. Author manuscript; available in PMC: 2010 Apr 9.

Published in final edited form as: J Chem Theory Comput. 2009 Apr 9;5(5):1301–1314. doi: 10.1021/ct9000153

Table II.

Summary of Lyn CD Activation/Deactivation Trajectories

Progress Variable	Method	Direction^a	Length (ns)	Force Constant (kcal/(mol·Å⁴))	Rate (Å/ps)	Color^b

MSID	TMD	A→I	0.16	-	0.1	black
		A→I	1.0	-	0.016	red

		I→A	0.16	-	0.1	green
		I→A	1.0	-	0.016	blue

	SMD	A→I	0.16	1000	0.1	black
		A→I	1.0	1000	0.016	red

		I→A	0.16	1000	0.1	green
		I→A	1.0	1000	0.016	blue

	BMD	A→I	1.9	1000	-	black
			1.5	2000	-	red
			1.5	3000	-	yellow
			1.3	5000	-	brown

		I→A	1.9	1000	-	green
			1.9	2000	-	blue
			1.7	3000	-	gray
			1.0	5000	-	purple

RMSD	TMD	A→I	0.2	-	0.03	black
		A→I	1.0	-	0.006	red

		I→A	0.2	-	0.03	green
		I→A	1.0	-	0.006	blue

A=active state; I=inactive state.

Coloring for Figure Figure 8(a)