Am I correct in saying now, from the following topology (exerpts), that
the virtual site VS will only interact with C3?
I guess I don't have to give the atom indices of this interaction in the
pair list which I use only for 1_4 interactions?
Can I use sigma and epsilon in the nonbond_params directive like in
atomtypes.
;Parameter level
[defaults]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
[atomtypes]
;type mass charge ptype sigma(nm)
epsilon(kjmol-1)
CB 12.011000 0.000000 A 0.355000 0.292880
CA 12.011000 -0.115000 A 0.355000 0.292880
HC 1.008000 0.115000 A 0.242000 0.125520
CU 13.019000 0.265000 A 0.350000 0.334720
NU 14.007000 -0.597000 A 0.325000 0.711280
CH 13.019000 0.332000 A 0.385000 0.334720
C3 15.035000 0.000000 A 0.390500 0.732200
C2 14.027000 0.000000 A 0.390500 0.493712
VS 0.0 0.0 V 0.0 0.0
[nonbond_params]
;i j func sigma epsilon
VS C3 1 0.1 0.03153
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