I’m minimizing the energy in a system of ozone molecules and water solvents, and the ozone molecules are placed above the water, and separated from the water, but the energy is minimized, and the chemical bonds of the ozone molecules break. What’s going on, please? Could it be the MDP file parameters
Bonds cannot break or form in classical MD simulations or any MM process. Likely you are just seeing some kind of strained configuration that your visualization software doesn’t understand. We will need more information, including the topology, images of what you’re seeing, and .mdp settings. The output of energy minimization (maximum force and potential energy, as printed by mdrun) would also be useful.