Equipartition test with OpenMM output. #252
Description
is there a way to to extract data files from MD simulation with openmm and run an equipartition test without getting a singular matrix error?
currently I ouput velocities and positions and I exclude from it Ions but still get a singular matrix warning
physical_validation.kinetic_energy.equipartition(strict=True) dies with
numpy.linalg.LinAlgError: Singular matrix whenever the OpenMM system
contains one-atom “molecules” (e.g. Na⁺ / Cl⁻).