[gmx-users] Generate non-bonded combinations

[lan hoa Trinh]

Dear Gromacs community,
I am using Gromacs to simulate a C-alpha structure and have the following
topology file (created by http://smog-server.org/).
[ defaults ]
 ;nbfunc comb-rule gen-pairs
           1           1 no

 [ atomtypes ]
  ;name  mass     charge   ptype c10       c12
 CA     1.000    0.000 A    0.000   0.167772160E-04

 [ moleculetype ]
 ;name   nrexcl
 Macromolecule           3

 [ atoms ]
 ;nr  type  resnr residue atom  cgnr charge  mass
     1  CA       1  ASN  CA       1   0.000   1.000
     2  CA       2  LEU  CA       2   0.000   1.000
     3  CA       3  LYS  CA       3   0.000   1.000
     4  CA       4  THR  CA       4   0.000   1.000
....

 [ pairs ]
 ; i j type and weights
     2     25 1   0.198921701E+01   0.132925132E+01
     2     27 1   0.582768432E+02   0.765215442E+02
     2     45 1   0.865830453E+01   0.776440056E+01
     3      7 1   0.143745898E+02   0.142660275E+02
     3      8 1   0.458838723E+02   0.574355228E+02
...
As I understand, VDW parameter will only be generated by grompp for pairs
of atoms which are defined in the directive [pairs]. When I use grompp, the
notification is:
Generated 1 of the 1 non-bonded parameter combinations.
Based on the above topology ([pairs]) i expected there are more non-bonded
combination generated. Can anyone help me to explain this?

Also:
[ atomtypes ]
  ;name  mass     charge   ptype c10       c12
 CA     1.000    0.000 A    0.000   0.167772160E-04
At first, I thought it meant that the pairs  which were not defined in the
directive [pairs] will be repulsive only, but they choose genpairs=no, so
it looks like there is nothing to do with the lines??

Please help me! Thanks in advance.
Best regards,
*Lan Hoa *