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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)
LASP (academic)
NAMD (free)
sGDML - Symmetric Gradient Domain Machine Learning
TINKER (free)
BerkeleyGW (academic)
ELSI - ELectronic Structure Infrastructure
ADC-connect - algebraic-diagrammatic construction (python)
ANT - nonadiabatic MD (academic)
CASINO - quantum MC (academic)
Dirac - relativistic effects (academic)
Forte - multireference quantum chemistry methods
libAtoms+QUIP - MD+TB
MCTDH - quantum MD (academic)
MS2 - MD for thermodynamics of liquids
MultiPsi - MCSCF (python)
NEXMD - nonadiabatic MD (free)
PYXAID - nonadiabatic MD (free)
QCManyBody - many-body expansion (python)
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)
JARVIS - Joint Automated Repository for Various Integrated Simulations (NIST)
MatCloud - based on VASP
Pymatgen - Python Materials Genomics
DAMASK - the Dusseldorf Advanced Material Simulation Kit
CAT - Compound Attachment Tool
LEADOMISE - workflow for directed medicinal chemistry design
TRAVIS - Trajectory Analyzer and Visualizer
MolSym - Python package for handling molecular symmetry
QSym2 - Quantum Symbolic Symmetry Analysis Program for Electronic Structure
SeeK-path - k-path finder and visualizer
ATAT - Alloy Theoretic Automated Toolkit
CREST - Conformer-Rotamer Ensemble Sampling 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)
Multiwfn - Multifunctional Wavefunction Analyzer
NBO6 - Natural Bond Orbital analysis (see also NBO5)
OpenMM - MD Toolkit (free)