When performing energy minimization of the MXene system (Ti₃C₂OH) using GROMACS, I observed that the potential energy becomes negative (approximately −10⁴) when no partial charges are assigned to the atoms. However, after assigning partial atomic charges obtained from the literature on MXene simulations, the minimized potential energy becomes strongly positive, on the order of 10⁷ , despite the system having an overall neutral charge. This discrepancy suggests that an issue may exist in the assigned charges or force-field parameters. It therefore raises the question of whether the simulation setup is physically consistent and whether subsequent simulations should proceed without further validation.
I don’t understand the cause of this phenomenon. I merely added the charge, and the charge originated from a piece of literature.（Poly(ionic liquid)-Armored MXene Membrane: Interlayer Engineering for Facilitated Water Transport）
Thank you for your suggestion. However, I am using a crystal CIF file, and the potential energy is positive when energy minimization occurs. Pre-equilibration seems to be supposed to be considered after energy minimization. I have recently started learning GROMACS. If there are any incorrect parts in my statement, please let me know.