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HyperChem (molecules only)
Schrodinger (Jaguar, Maestro, Macromodel)
Spartan (molecules only)
Atomistix ToolKit (academic)
Gabedit (free)
Pyiron (IDE for computational materials science)
WebMO (free online version requiring Perl and Apache server)
Rosetta (academic, proteins and nucleic acids)
BigDFT (free, wavelets)
CP2K (free, GTO and PW +MD +TB +classical MD)
CRYSTAL (GTO)
FHI-aims (numerical AO)
Gaussian (GTO)
NWChem (academic)
Octopus (grid-based +TDDFT)
Columbus (academic, MRCI)
Firefly (academic)
FreeON (free, linear scaling +PBC +MD)
GAMESS (academic)
Molpro (MRCI)
ABINIT (free)
CASTEP (+MD)
Conquest (academic, linear scaling)
GPAW (grid-based projector-augmented wave method)
ONETEP (Wannier, linear scaling)
Quantum ESPRESSO (free)
SIESTA (academic, optimized LCAO, linear scaling + MD)
VASP (+MD)
WIEN2k (augmented PW and local orbitals)
Yambo (free, post-DFT)
AMPAC (+GUI)
MOPAC (academic)
DFTB+ (academic +DFT)
xtb (academic)
NEMO-3D (free)
Plato (academic +DFT)
AMBER (biomolecules)
GROMACS (free)
GULP (academic)
LAMMPS (free)
NAMD (free)
TINKER (free)
BerkeleyGW (academic)
ADC-connect - algebraic-diagrammatic construction (python)
ANT - nonadiabatic MD (academic)
CASINO - quantum MC (academic)
Dirac - relativistic effects (academic)
libAtoms+QUIP - MD+TB
MCTDH - quantum MD (academic)
MS2 - MD for thermodynamics of liquids
PYXAID - nonadiabatic MD (free)
QMCPACK - quantum MC (free)
QWalk - quantum MC (free)
TurboRVB - quantum MC (free)
AiiDA - Automated Interactive Infrastructure and Database for Computational Science
ASE - Atomic Simulation Environment
ESL - Electronic Structure Library (CECAM)
MatCloud - based on VASP
Pymatgen - Python Materials Genomics
DAMASK - the Dusseldorf Advanced Material Simulation Kit
ATAT - Alloy Theoretic Automated Toolkit
CAT - Compound Attachment Tool
FDA - Computation of Atomic Orbitals (free, Density Functional method and the Xalpha functional)
LocVib - vibrations localization
Molecular Dynamics Studio - simplifies MD in LAMMPS
MOVIPAC - vibrational spectroscopy (numerical derivatives)
NBO6 - Natural Bond Orbital analysis (see also NBO5)
OpenMM - MD Toolkit (free)
SeeK-path - k-path finder and visualizer
TRAVIS - Trajectory Analyzer and Visualizer