Table 1:

The scaling behavior/λ-dependence of the weight functions in eq. 4, controlled by the gti_add_sc flag, for different energy terms and regions/interactions in AMBER22^a.

Weight Symbol	Energy Term Abbreviation	Region / Interaction	gti_add_sc flag
			1	2	3	4	5	6
$W_{\{0/1\},bond}^{SC}$	bond	SC	P	P	P	P	P	P
$W_{\{0/1\},ang}^{SC}$	ang	SC	P	P	P	P	P	P
$W_{\{0/1\},tor}^{SC}$	tor	SC	P	P	P	S	S	S
$W_{\{0/1\},dir}^{SC}$	dir	SC	P	S	S	P	S	S
$W_{\{0/1\},1-4Ele}^{SC}$	1–4 Ele	SC	P	S	S	S	S	S
$W_{\{0/1\},LJ}^{SC}$	LJ	SC	P	P	S	P	P	S
$W_{\{0/1\},1-4LJ}^{SC}$	1–4 LJ	SC	P	P	S	S	S	S
$W_{\{0/1\},bond}^{SC/(CC+I)}$	bond	SC/(CC+I)	Special treatmentb
$W_{\{0/1\},ang}^{SC/(CC+I)}$	ang	SC/(CC+I)	Special treatmentb
$W_{\{0/1\},tor}^{SC/(CC+I)}$	tor	SC/(CC+I)	Special treatmentb
$W_{\{0/1\},dir}^{SC/(CC+I)}$	dir	SC/(CC+I)	S	S	S	S	S	S
$W_{\{0/1\},1-4Ele}^{SC/(CC+I)}$	1–4 Ele	SC/(CC+I)	S	S	S	S	S	S
$W_{\{0/1\},LJ}^{SC/(CC+I)}$	LJ	SC/(CC+I)	S	S	S	S	S	S
$W_{\{0/1\},1-4LJ}^{SC/(CC+I)}$	1–4 LJ	SC/(CC+I)	S	S	S	S	S	S
$W_{\{0/1\}}^{CC+I}$	all	CC+I	S	S	S	S	S	S
W {0/1},rec	rec	all	S	S	S	S	S	S

^aEnergy terms and interacting regions are defined in the text (and also Tables S1 and S2 of the Supporting Information).

Flags:

S: Scaled (S) with λ (weight in eq 9 set to the λ-dependent weight function) and the corresponding energy term is NOT present in the dummy state.

P: Not scaled with λ (weight in eq 9 set to 1) and corresponding energy term is present (P) in the dummy state.

^bBonded terms between the SC and (CC+I) regions require special treatment such that they obey certain conditions in order that the ensembles generated in the state that contains “dummy atoms” reproduce the same potential of mean force on the real atoms as the real system without the dummy atoms. A discussion of the energy term requirements that satisfy these conditions has been made by Boresch and Karplus^26,27 and Roux and co-workers,^25,28 and recently discussed in depth in the context of alchemical transformations.²⁹