. 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 I.

Summary of BdpA Unfolding Trajectories

Progress Variable	Method	Length (ns)	Force Constant (kcal/(mol Å²))	Rate (Å/ps)	#^a	Code

h	TMD	0.5	-	0.1	2	hT1
		2	-	0.025	2	hT2
		10	-	0.005	2	hT3

	SMD	0.5	50	0.1	2	hS1
		2	50	0.025	2	hS2
		10	50	0.005	2	hS3

	BMD	0.5	50	-	2	hB1
		2	20	-	2	hB2
		10	8	-	2	hB3

R_g	TMD	0.5	-	0.05	2	RT1
		2	-	0.0125	2	RT2
		10	-	0.0025	4	RT3

	SMD	0.5	5000	0.05	2	RS1
		2	5000	0.0125	2	RS2
		10	5000	0.0025	4	RS3

	BMD	0.5	5000	-	2	RB1
		2	400	-	2	RB2
		10	110	-	4	RB3

Number of independent trajectories that were calculated