[gmx-users] gen-pairs

[Alexander Alexander]

Dear Gromacs user,

Surprisingly I am wondering why I have no warning while I assigned "NO" for
the "gen-pairs" in [ default ] section of my .top file, although I have no
pair type neither in my .top file nor in ffnonbonded.itp for these atoms?

I am referring to this statement in gromacs-manual: "When gen-pairs is set
to “no,” grompp will give a warning for each pair type for which no
parameters are given".

My system is a pure transition metal solid that it's topol file comes below:

topol.top
-------------------------
; topol file for A3B
; force field parameters in below
[ Defaults ]
;  nbfunc        comb-rule       gen-pairs       fudgeLJ  fudgeQQ
     1                   3                         no
0.5       0.5

[ atomtypes ]
;   name      mass        charge    ptype       sigma           epsilon
     A            32.00          0.21          A        2.27357e-01
25.1
     B            6.700         -0.63          A        1.714534e-01    4.4

[ moleculetype ]
; Name            nrexcl
  A                       1
[ atoms ]
;  nr     at type  resnr   residue   atom name   cgnr     charge       mass
   1            A         1          A                   A
1       0.21           32.00

[ position_restraints ]
; ai  funct  fcx    fcy    fcz
   1    1    2000   2000   2000

[ moleculetype ]
; Name            nrexcl
  B               1
[ atoms ]
;  nr     at type  resnr   residue   atom name   cgnr     charge       mass
   1                              B        1          B          B
1      -0.630         6.70

[ position_restraints ]
; ai  funct  fcx    fcy    fcz
   1    1    2000   2000   2000

[ system ]
; Name
   A3B

[ molecules ]
;mol_name number
   A    14400
   B     4800
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