[gmx-users] virtual sites set up for topology file

[Gavin Melaugh]

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