I am optimizing an anthracene molecule using the Bordat force field (doi 10.1063/1.3093065), and I’m having some difficulty understanding the output. For configuration 1, there is an energy contribution from the 4 body terms, but these disappear after relaxation. This shouldn’t be the case, since the most terms are out of equilibrium (the equilibrium dihedral angles are all 0 or 180 degrees).

Hi Levi. Your initial structure has a carbon atom which is distorted out of the plane. On relaxation this goes back to where it should be. Given that the torsional potentials have equilibrium angles of 0 and 180 and the structure of anthracene has torsions of 0 and 180, everything is exactly as it should be & there is no problem.
Regards Julian