Molecular dynamics (Energy minimization, trajectories, approximations)

Quantum Electrodynamics (QED) Schwinger

Born-Oppenheimer Approximation

Quantum Engines Molecular Orbital Methods

Semiempirical Hartree-Fock methods

Modified Intermediate Neglect of Differential Overlap (MINDO)

Modified Neglect of Diatomic Overlap (MNDO) - AMPAC, MOPAC

SemiChem Austin Model 1 (SAM1) - Explicitly treats d-orbitals.

ab initio Hartree-Fock programs:

GAMESS, Gaussian

Semiempirical Engines (Molecular Mechanics) from above & spectroscopy

AMBER, Discover, SYBYL, CHARMM, MM2, MM3, ECEPP.

(Chemistry at HARvard Molecular Mechanics),

http://cmm.info.nih.gov/modeling/guide_documents/tocs/computation_software.html

http://www.foresight.org/Nanosystems/toc.html

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