has_barostat has_thermostat has_integrated_atom has_ensemble has_integrator has_coordinates has_COM_coordinates has_bond has_angle has_dihedral first_atom second_atom third_atom fourth_atom has_interaction_potential corresponds_to_bond corresponds_to_angle corresponds_to_bond has_component has_computational_input has_computational_output has_experimental_input has_experimental_output has_property has_structural_entity has_structural_atom has_structural_functional_group has_structural_functional_group has_structural_molecular_system is_structural_entity_of is_structural_atom_of is_structural_particle_of is_structural_functional_group_of is_structural_functional_group_of has_structure is_part_of is_atom_of is_particle_of is_functional_group_of is_molecular_system_of has_subunit has_atom has_particle has_functional_group has_molecular_system is_computed_by is_measured_by use_algorithm use_computational_method use_experimental_method atomic_number algorithm_type at charge composition pressure target_pressure temperature target_temperature time_constant X Y Z polar_angle azimuthal_angle real_part i j k element_11 element_12 element_13 element_21 element_22 element_23 element_31 element_32 element_33 interaction_potential_type dihedral_coefficient_1 dihedral_coefficient_2 dihedral_coefficient_3 dihedral_coefficient_4 dihedral_coefficient_5 dihedral_coefficient_6 equilibrium_value bond_type epsilon equilibrium_distance force_constant sigma energy_threshold formula ID log max_number_of_steps number_of_molecules number_of_atoms number_of_timesteps purpose radial_distance spacegroup symbol unit value Material Structure Crystal MolecularAggregate StructuralEntity Atom MolecularSystem Particle FunctionalGroup MaterialProperty ChemicalProperty ElectroMagneticProperty MechanicalProperty Simulation ComputationalMethod Algorithm MolecularDynamics Optimizer StructureManipulation SimulationEnsemble NPT NVT NVE ExternalCoupling Barostat Thermostat Integrator Experiment Continuant ContinuantFiatBoundary Process ExperimentalMethod ElectricalMethod TOF OpticalMethod Coordinates CartesianCoordinates SphericalCoordinates Orientation Quaternion RotationMatrix TopologicalEntities Bond Angle Dihedral LatticeParameter InteractionPotential MolecularMechanics BondedPotential NonBondedPotential QuantumMechanics DFT HartreeFock PotentialComponent FourBody ThreeBody TwoBody