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Sometimes this can be worked around by temporarily using extremely stiff force constants for bonds/angles/dihedrals/impropers to keep the molecules “near rigid”.
Could be by it is not likely.
very unlikely
Most likely candidate for a problem is your data file, e.g. the box dimensions are incorrect not large enough or molecules are overlapping. This can be tested by first creating a system with few molecules (like 1 or 2) and checking what the energy per molecule would be like. Then you can gradually increase to number of molecules until you see a significant difference. That is where you need to look at the file more carefully.
Another option would be to use a different strategy to create the system, e.g. through using a molecule file and then create_atoms from within LAMMPS with the “overlap” parameter set to guarantee a minimum distance between molecules.