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I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input.

         12  molden generated tinker .xyz (oplsaa param.)
  1  C     0.000000    1.402720    0.000000     90   2   3  11
  2  H     0.000000    2.490290    0.000000     91   1
  3  C    -1.214790    0.701360    0.000000     90   1   4   5
  4  H    -2.156660    1.245150    0.000000     91   3
  5  C    -1.214790   -0.701360    0.000000     90   3   6   7
  6  H    -2.156660   -1.245150    0.000000     91   5
  7  C     0.000000   -1.402720    0.000000     90   5   8   9
  8  H     0.000000   -2.490290    0.000000     91   7
  9  C     1.214790   -0.701360    0.000000     90   7  10  11
 10  H     2.156660   -1.245150    0.000000     91   9
 11  C     1.214790    0.701360    0.000000     90   1   9  12
 12  H     2.156660    1.245150    0.000000     91  11

I ran ANALYZE binary with this file and oplsaa.prm using the D option and then it gives me the details of each interaction.

The charge-charge interactions are given as

Charge          1-C        6-H            -0.12   0.12     3.4150     -0.6430
Charge          1-C        7-C            -0.12  -0.12     2.8054      0.7827
Charge          1-C        8-H            -0.12   0.12     3.8930     -1.1280
Charge          1-C       10-H            -0.12   0.12     3.4150     -0.6430
Charge          2-H        4-H             0.12   0.12     2.4903      0.8817
Charge          2-H        5-C             0.12  -0.12     3.4150     -0.6430
Charge          2-H        6-H             0.12   0.12     4.3133      1.0181
Charge          2-H        7-C             0.12  -0.12     3.8930     -1.1280
Charge          2-H        8-H             0.12   0.12     4.9806      0.8817
Charge          2-H        9-C             0.12  -0.12     3.4150     -0.6430
Charge          2-H       10-H             0.12   0.12     4.3133      1.0181
Charge          2-H       12-H             0.12   0.12     2.4903      0.8817
Charge          3-C        8-H            -0.12   0.12     3.4150     -0.6430
Charge          3-C        9-C            -0.12  -0.12     2.8054      0.7827
Charge          3-C       10-H            -0.12   0.12     3.8930     -1.1280
Charge          3-C       12-H            -0.12   0.12     3.4150     -0.6430
Charge          4-H        6-H             0.12   0.12     2.4903      0.8817
Charge          4-H        7-C             0.12  -0.12     3.4150     -0.6430
Charge          4-H        8-H             0.12   0.12     4.3133      1.0181
Charge          4-H        9-C             0.12  -0.12     3.8930     -1.1280
Charge          4-H       10-H             0.12   0.12     4.9806      0.8817
Charge          4-H       11-C             0.12  -0.12     3.4150     -0.6430
Charge          4-H       12-H             0.12   0.12     4.3133      1.0181
Charge          5-C       10-H            -0.12   0.12     3.4150     -0.6430
Charge          5-C       11-C            -0.12  -0.12     2.8054      0.7827
Charge          5-C       12-H            -0.12   0.12     3.8930     -1.1280
Charge          6-H        8-H             0.12   0.12     2.4903      0.8817
Charge          6-H        9-C             0.12  -0.12     3.4150     -0.6430
Charge          6-H       10-H             0.12   0.12     4.3133      1.0181
Charge          6-H       11-C             0.12  -0.12     3.8930     -1.1280
Charge          6-H       12-H             0.12   0.12     4.9806      0.8817
Charge          7-C       12-H            -0.12   0.12     3.4150     -0.6430
Charge          8-H       10-H             0.12   0.12     2.4903      0.8817
Charge          8-H       11-C             0.12  -0.12     3.4150     -0.6430
Charge          8-H       12-H             0.12   0.12     4.3133      1.0181
Charge         10-H       12-H             0.12   0.12     2.4903      0.8817

Thus, There are only 36 interactions. I thought that the total number of interactions would be 12*11/2=66, but it is a much smaller number. The number of vdW interactions is also the same, 36. What is going on? It is an isolated molecule, so I believe that there's no cutoff issue.

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The charge-charge interactions are only including things which aren't "bonded", this includes angles, and sometimes 1,4 Torsions. This is because the electrostatic interaction is already included in the parameterization of those potentials.

So in your data, this is why we see charge-charge parameters between carbon and a bunch of hydrogens, because they aren't bonded.

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  • $\begingroup$ I checked Bond and Angle type interactions and found that charge-charge interactions are only counted when each pair doesn't appear in Bond and Angle type interactions, as you said. Thank you. $\endgroup$
    – Patche
    Jan 30 at 8:23

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