Nonbonded intramolecular interactions

Dear Cassandra authors, dear community,

when I simulate only a single molecule in the box (no LR corrections) in version 1.1 I don't get equal Energy_Total and Energy_Intra. I suspect non-bonded intramolecular contributions are not included in Energy_Intra despite Cassandra manual says they are. When I add Energy_Intra, Energy_LJ and Energy_Elec, I get exactly Energy_Total. Also, looking into the source code, file energy_routines.f90 , one can find the line

which also seems to suggest non-bonded (vdw and q) interactions are not included in intra term.

Could you either confirm or refute my view?
Thanks, Jan

The Intra molecular energy only includes the bond energy (0) + bond angle energy + dihedral angle energy + improper angle energy. It does not include the inra molecule vdw or q.

However, mine seems to add up

Total system energy is 378936.094
Intra molecular energy is -38466.638
Bond energy is 0.000
Bond angle energy is 131166.847
Dihedral angle energy is -169633.485
Improper angle energy is 0.000
Intra molecule vdw is -20699.451
Intra molecule q is 470498.175
Inter molecule vdw is -685.945
Inter molecule q is 3716966.778
Number of vectors is 35300
Reciprocal ewald is 37161.213
Self ewald is -3785838.038

Bond energy (0) + Bond angle energy (131166. + Dihedral angle energy (-169633) + Intra molecule vdw (-20699.451) + Intra molecule q (470498.175) + Inter molecule (vdw) (-685.945) + Inter molecule q (3716966.778) + Reciprocal ewald (37161.213) + Self ewald (-3785838.038) = 378936.094.

This number matches what is printed in *prp (with the unit change from atomic to kJ/mol)...factor of 100.

jdmoore wrote: The Intra molecular energy only includes the bond energy (0) + bond angle energy + dihedral angle energy + improper angle energy. It does not include the inra molecule vdw or q.

Yes, that is consistent with my observation. However, it contradicts Cassandra 1.1 manual, which explicitly says:
"Energy_Intra: Total intramolecular energy of the system including bonded and non-bonded interactions in kJ/mol"

Hi Ryan,
thank you very much for your response. I am glad my understanding was correct. I wanted to be sure I am evaluating appropriate intramolecular energy to compare between ideal gas and condensed phase.
Best regards
Jan