. 2021 May 13;17(5):e1008936. doi: 10.1371/journal.pcbi.1008936

Table 1. Percentage of improved models after MD refinement.

ΔRMSD_LIG / Å^a	OPLS / %	CHARMM / %	OPLS (restrained) / %^b
< 0.0	50	73	60
< –0.5	30	57	37
< –1.0	17	30	23
ΔRMSD_TM / Å^a
< 0.0	3	37	43
< –0.05	3	20	23
< –0.1	3	17	10
ΔRMSD_EL2 / Å^a
< 0.0	50	50	70
< –0.5	37	37	53
< –1.0	23	27	27

^a Calculated as the difference in RMSD between the best MD refined (selected from the centroids representing the five largest clusters for each model) and the initial structure (ΔRMSD = RMSD_{MD refined}−RMSD_{Initial model}).

^b Simulations were performed with restraints on C_α atoms in the TM region.