HyperChem assigns atom types and parameters not normally available to MM2, extending the range of chemical compounds this force field can accommodate. The facility in HyperChem that constructs 3D models of chemical structures from 2D drawings. The model builder also assigns atom types for the currently active force field and can automatically add hydrogens to satisfy valence requirements. Molecular Dynamics Calculations simulating the motion of each atom in a molecular system at a fixed energy, fixed temperature, or with controlled temperature changes. Molecular Mechanics Various methods for calculating the potential energy of molecular systems as a function of the coordinates of their atomic nuclei, neglecting explicit treatment of electrons.
Electronic effects are implicit in the analytic functional forms and parameterization.
All methods use empirical data to determine individual force constants and equilibrium values for each geometric quantity. OPLS Optimized Potentials for Liquid Simulations. A molecular mechanics method, or force field, for chemical calculations. Developed for proteins and nucleic acids. A predefined named selection identifying the atoms in the named selection plus the centre of mass of the selected atoms.