TABLE 3.

Summary of calculations (protocols) using elastic network models

Notation	Model	Pulling set S*	Parameters†
ECO-1-1	United atom ENM	TM1 (16–40) & TM2 (77–106) backbone
			k = 0.41
ECO-1-2	United atom ENM	Backbone |z| < 20 Å	Same as ECO-1-1
ECO-1-3	United atom ENM	TM2 (77–106) backbone	Same as ECO-1-1
ECO-2-1	United atom ENM + elastic lipid	Outer membrane shell (2 Å); solving Eq. 31	Same as ECO-1-1, except
			k = 4.49;
ECO-3-1	United atom ENM + elastic lipid	Outer membrane shell (2 Å); explicit minimization	Same as ECO-1-1, except k = 4.49;

^*In all calculations, the ends of the external harmonic pulling springs are displaced in a radially outward fashion, and these pulling springs are free to move in the z-direction. The membrane center is at z=0.0 Å.

^†The force constants for the elastic springs (γ) and the harmonic pulling springs (k) are in kcal/(mol·Å²); the cutoffs (R_cut) are in Å.