. Author manuscript; available in PMC: 2018 Apr 24.

Published in final edited form as: Biochemistry. 2018 Feb 15;57(9):1533–1541. doi: 10.1021/acs.biochem.7b01248

Table 1.

Summary of 10 GaMD Simulations Performed on Binding of the XK263 Ligand Molecule to the HIV Protease^a

	duration (ns)	ΔV_total (kcal/mol)		ΔV_dih (kcal/mol)		minimum ligand RMSD (Å)
	duration (ns)	ΔV_avg	σ_Δ_V	ΔV_avg	σ_Δ_V	minimum ligand RMSD (Å)
Sim1	2500	7.41	2.93	6.42	2.45	2.26
Sim2	2500	7.43	2.94	6.59	2.48	2.73
Sim3	1445	7.42	2.93	6.44	2.45	7.69
Sim4	2434	7.46	2.95	6.17	2.38	8.74
Sim5	2436	7.48	2.95	6.62	2.47	5.40
Sim6	500	7.42	2.94	6.61	2.47	6.36
Sim7	500	7.44	2.94	6.57	2.48	17.46
Sim8	500	7.43	2.93	6.3	2.41	19.37
Sim9	500	7.42	2.93	6.29	2.42	21.55
Sim10	500	7.43	2.94	6.09	2.37	20.72

ΔV_total and ΔV_dih are the boost potential applied to the total potential and dihedral energy terms of the system, respectively.