Software for Atomic Scale Education and Research
This page lists links to the web sites which have information about software and software developers (academic centers, national labs, industrial companies and individuals). If such information is available we indicate whether software is non-commercial (but you may need to sign a license agreement), commercial or semi-commercial (e.g. free for academia and commercial for companies). Some software packages include several applications, e.g. visualization and classical and quantum mechanical computational engines. Such programs can be listed in several sections below, which are grouped as:
- Visualization & Design
- Classical Mechanics & Molecular Dynamics
- Quantum Mechanics
- Non-Profit Research Centers
- Companies
- Forums
- Databases & Supplementary Software
Design and Visualization
- Agile Molecule (Biomolecular simulations; Non-commercial)
- ADFGUI (GUI to ADF, BAND, DFTB, MOPAC2009, ReaxFF, COSMO-RS; commercial))
- ArgusLab (Non-commercial)
- Aten (Non-commercial)
- Avogadro (Non-commercial)
- Bodil (Non-commercial)
- BRAGI (Proteins visualization; Non-commercial)
- Chimera (Semi-commercial)
- Force Field Explorer (Visualizer for Tinker; non-commercial)
- Gabedit (Non-commercial)
- GAMGI (Non-commercial)
- GaussView (Commercial)
- HyperChem (Commercial)
- ICM-Browser (Semi-commercial)
- iMol (Molecular visualizer for Mac OSX; Non-commercial)
- Indigo 3D Molecular Builder (Commercial)
- IQmol (Non-commercial, an interface to Q-Chem)
- Jmol (Non-commercial)
- Maestro (Commercial)
- MacMolPlt (Non-commercial)
- MAPS (Commercial)
- MarvinSpace (Commercial)
- Materials Studio (Commercial)
- MedeA (Commercial; classic forcifield, GUI to VASP)
- Mercury (Viewer for crystals; commercial)
- Molden (Non-commercial)
- Molegro (Commercial)
- MolMol (Non-commercial)
- MovieMol (Molecular view and animation; semi-commercial)
- NAMOT (Nuclear acids viewer; non-commercial)
- QuteMol (Molecular viewer; non-commercial)
- PyMOL (Molecular viewer; non-commercial)
- RasMol (Molecular viewer; non-commercial)
- SageMD (Viewer and database of periodic structures; semi-commercial)
- Vega ZZ (Semi-commercial)
- VMD (Molecular viewer; non-commercial)
- XCrysDen (Crystal viewer; non-commercial)
- Yasara (Biomolecular viewer; commercial)
- 3DMolSym (Commercial; symmetry visualization)
Classical Mechanics and Molecular Dynamics
- Amber (Commercial)
- AMMP (Non-commercial)
- Boss (Commercial)
- CHARMM (Commercial)
- Desmond (Non-commercial)
- EGO (Biomolecular MD; non-commercial)
- Gromacs (Non-commercial)
- GROMOS (Non-commercial)
- GULP (Periodic MM/MD; semi-commercial)
- HyperChem (commercial)
- Lammps (Non-commercial)
- MacroModel (Commercial)
- MDTools (Set of programs and scripts for MD; non-commercial)
- MMTK (MD Toolkit; non-commercial)
- Moldy (Non-commercial)
- Moscito (Gas and condensed phase MD; non-commercial)
- Music (MD and Monte Carlo code; non-commercial)
- NAMD (Semi-commercial)
- PyMD (Python library for flexible multi-scale molecular dynamics simulation; non-commercial)
- ReaxFF (Reactive molecular dynamics; semi-commerical)
- Tinker (Non-commercial)
- SageMD (Semi-commercial)
- XMD (non-commercial)
- Yasara (commercial)
Quantum Mechanics
- Abinit (Periodic DFT; semi-commercial)
- ACES (Ab initio molecular code; semi-commercial)
- ADF (Molecular DFT; commercial)
- AMPAC (Semi-empirical; commercial)
- Amsol (semi-empirical; semi-commercial)
- BAND (Periodic DFT; commercial)
- Boss (Commercial)
- CASINO (Quantum Monte Carlo program; non-commercial)
- CASTEP (Periodic DFT; commercial for all but UK academia)
- CFOUR (Coupled Cluster methods; non-commercial)
- CPMD (Periodic DFT; Semi-commercial)
- CRYSTAL (Periodic DFT; commercial)
- Dalton (Molecular ab initio; non-commerical)
- deMON (Molecular DFT; Semi-commercial)
- DFTB (Approximate DFT; semi-commercial)
- Dirac (Atomic and molecular relativistic code; non-commercial)
- FHI98md (Periodic DFT; non-commercial)
- GAMESS (ab initio; non-commercial)
- Gaussian (Ab initio molecular and periodic systems; commercial)
- GPAW (Grid-based PAW DFT; non-commercial)
- HyperChem (semi-empirical; commercial)
- Jaguar (Ab initio molecular; commercial)
- MCTDH (Time dependent Schroedinger equation; non-commercial)
- Molcas (Molecular ab initio; commercial)
- Molpro (Molecular ab initio; commercial)
- MOPAC (Semi-empirical QM; non-commericial)
- NWChem (Molecular and periodic systems; Ab initio and DFT; non-commercial)
- Octopus (TDDFT; non-commercial)
- OpenMX (DFT; non-commercial)
- ORCA (Ab Initio,DFT, semiempirical; free for academic users)
- PC Gamess (Ab Initio; non-commercial)
- Q-Chem (Ab initio and DFT; commercial)
- Turbomole (Molecular ab initio code; commercial)
- Siesta (Periodic DFT; semi-commercial)
- VAMP (Semi-empirical QM; commercial)
- VASP (Plane wave periodic DFT; commercial)
- WIENek (DFT periodic systems; commercial)
Companies
- Accelrys (Visualization, classical and quantum mechanics, mesoscale)
- Astonis (Integrated computational chemistry tools)
- ATel – Commercial software tools for chemistry and engineering education
- Cemcomco (software for drug discovery, biotechnology, and chemistry)
- ChemAxon (Software developer for bio and pharmaceutical industries)
- Computational Chemistry (Reseller)
- COSMOlogic (Computational chemistry and fluid thermodynamics)
- Dotmatics (Software tools for scientists in biotech/pharma space)
- FQS Poland (Provider of molecular modeling software)
- HyperCube (Developer and provider of HyperChem)
- Indigo Instruments (Molecular models and more)
- Kintech (Provider of software for chemical kinetics)
- Materials Design (MedeA package, consulting)
- Molecular-Conceptor.com (Drug design)
- Molsoft (Molecular software and consulting)
- Nano & Giga Solutions (Computational materials design; consulting)
- Reaction design (Chemical kinetics software provider)
- Schrodinger (Software provider for biomolecular design)
- Scienomics (Molecular modeling software provider)
- Scientific Computing & Modeling (Quantum mechanics of molecules and crystals)
- Seascape (Molecular modeling software and consulting)
- SCM (Molecular modeling software)
- Semichem (Provider of AMPAC and Codessa)
- SymBioSys (Software provider for drug design)
- Trypos (Modeling and consulting for biomolecular design)
- Wavefunction, Inc. (Molecular simulation software provider and consulting)
Non-Profit Research groups
- CECAM (European Center for Atomic and Molecular Computations)
- Center for Computational Materials Science (Naval Research Laboratory)
- Centre for Molecular and Biomolecular Informatics (Dutch national centre for computational molecular sciences)
- Center for Structural Biology (Yale University)
- Collaborative Computational Projects (UK)
- CompuChem (Education & visualization for chemistry)
- CSE-Online (Grid computing)
- Mark Gordon’s Quantum Theory Group
- Minnesota Computational Chemistry Group
- Network for Computational nanotechnology
- RBVI (Resource for Biocomputing, Visualization, and Informatics at UCSF)
- Quantum Theory Project (The whole spectrum of QM and CM/MD expertise)
- Science & Technology Council (UK)
- Theoretical and Computational Biophysics Group (University of Illinois Urbana-Champaign)
- Theory of Condensed Matter (University of Cambridge)
Forums
- Computational Chemistry List (all areas of computational chemistry and materials design, open positions)
- Dirac Program Mailing List
- Forum and discussions about Molecular Modelling and Quantum Chemistry
- Gamess Program Discussion Group
- iOpenShell (Electronic structure and quantum chemistry)
- Molecular Graphics and Modeling Society
- Molecular Modeling Community
- Siesta Program Mailing List
Databases & Supplementary Tools (beyond atomistics)
- ADF COSMO-RS (Fluid thermodynamics; commercial)
- Almond (QSAR)
- Babel (Format converter of molecular coordinates)
- Bioclipse (QSAR)
- BKChem (Drawing chemical formulas)
- Cambridge Crystallographic Data Center
- Cameo (Expert system for organic reactions)
- Chemistry Links (The list of links to chemistry software, companies, etc.)
- Chemkin (Chemical Kinetics)
- Codessa (QSAR)
- Computational Chemistry at NIST (Comparison and benchmark database)
- Crystal and Ionic Radii
- Debyer (Calculation of diffraction patterns)
- Dragon (QSAR)
- ECChem++ (Computational Electrochemistry)
- Khimera (Chemical kinetics software which uses quantum mechanics input)
- Kintecus (Chemical kinetics)
- Linux4Chemistry (List of computational chemistry software)
- Mexico (Simulator of NMR spectra)
- Minerology Database
- MMC (Metropolis Monte Carlo program)
- Molegro (Software for drug discovery)
- NIST Chemistry Web Book
- Open Babel (Chemistry toolkit; non-commercial)
- OpenMM (Library of tools for molecular mechanics; non-commercial)
- POLYRATE (Chemical kinetics)
- SmiLab (Platform independent, rapid combinatorial library enumeration)
- Web Links to Computational Chemistry Software
- WODCA (Computer assisted reaction design)
- WWW-MINCRYST (Inorganic crystals)