molsysmt.molecular_mechanics.get_non_bonded_potential_energy#

molsysmt.molecular_mechanics.get_non_bonded_potential_energy(molecular_system, selection='all', selection_2=None, platform='CPU', engine='OpenMM', syntax='MolSysMT', skip_digestion=False)[source]#

Calculating non-bonded interaction potential energy between selections or pairwise across structures.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • selection_2 (str, list, tuple, or numpy.ndarray, default=None) – Second selection string or boolean/integer array.

  • platform (str, default='CPU') – OpenMM platform name (‘Reference’, ‘CPU’, ‘CUDA’, ‘OpenCL’).

  • engine (object, default='OpenMM') – Argument engine.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

Non-bonded potential energy interaction values in canonical units (kJ/mol).

Return type:

quantity or dict

Added in version 1.0.0.