Table 1.

Results of 5 targets from DUD-E dataset comparing all-heavy-atom RMSD of the ligand-binding-site (LBS) residues across 5 different simulation programs.^a

PDB	Program	LBS all-heavy-atom RMSD
		Initial	Method 1b	Method 2c	Controld
2nnq	NAMD	1.99	1.10	1.48	2.10
	AMBER	1.99	1.18	1.46	2.04
	GROMACS	1.99	1.04	1.48	2.55
	OpenMM	1.99	1.03	1.32	2.17
	GENESIS	1.99	1.00	1.22	2.01
1h00	NAMD	2.13	1.06	1.28	2.07
	AMBER	2.13	1.05	1.15	2.91
	GROMACS	2.13	1.05	1.19	2.25
	OpenMM	2.13	1.12	1.44	2.04
	GENESIS	2.13	1.15	1.37	2.61
2fsz	NAMD	2.15	1.32	1.68	2.37
	AMBER	2.15	1.44	1.77	2.49
	GROMACS	2.15	1.32	1.52	1.97
	OpenMM	2.15	1.35	1.65	2.04
	GENESIS	2.15	1.45	1.76	2.10
3m2w	NAMD	2.35	1.28	1.75	2.36
	AMBER	2.35	1.34	1.82	2.48
	GROMACS	2.35	1.28	1.68	1.96
	OpenMM	2.35	1.31	1.77	2.18
	GENESIS	2.35	1.24	1.56	2.35
3bwm	NAMD	3.43	1.75	2.60	3.81
	AMBER	3.43	1.82	2.54	3.67
	GROMACS	3.43	1.65	2.22	4.21
	OpenMM	3.43	1.68	2.55	3.74
	GENESIS	3.43	1.77	2.29	3.44

^aImproved cases with lower RMSD are highlighted in bold.

^bMethod 1 using both Cα and SC-COM distance restraints.

^cMethod 2 using Cα-only distance restraints.

^dControl simulations without distance restraints.