. Author manuscript; available in PMC: 2019 Nov 6.

Published in final edited form as: J Chem Theory Comput. 2019 Sep 17;15(10):5543–5562. doi: 10.1021/acs.jctc.9b00401

Table 3:

Ab initio QM/MM simulation and reanalysis rates of the bound and unbound-state simulations used to calculate the ligiand binding free energies. The columns of CPU cost are the number of wallclock hours required to calculate $Δ A_{b}^{QM ∕ MM}$ using 1 node to produce 200 ps of sampling for the MM′→ QM transformations. QM/MM simulations are performed on a single node equipped with two, 18-core Intel Xeon E5-2695 v4 processors running at 2.1 GHz.

Ligand	Simulation Rate ps day⁻¹		Reanalysis Rate ns day⁻¹		CPU cost wallclock hours
Ligand	L∙P	L+P	L∙P	L+P	BBQm*	EA*
BNZ	131	147	66	74	69.4	0.1
PXY	63	65	32	33	150.3	0.3
OXE	60	62	30	31	157.7	0.3
BZF	60	61	30	31	159.0	0.3
DEN	53	54	27	27	179.8	0.4
IND	56	57	28	29	170.3	0.3
N4B	36	36	18	18	267.2	0.5
I4B	34	34	17	17	282.9	0.6