| Abalone | Y | Y | Y | Y | Y | Y | I | Y | Y | Biomolecular simulations, protein folding. | Free | Agile Molecule |
| ACEMD[1] | | | Y | Y | | | | | Y | Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA. | Basic version free. Commercial version available. | Acellera Ltd |
| ADUN[2] | | | Y | Y | | | Y | Y | Y | Charmm, AMBER, user specified (through force field markup language, FFML), QM/MM calculations with Empirical Valence Bond (EVB); Framework based (GNUStep/cocoa); SCAAS for spherical boundary conditions | Free | adun.imim.es |
| AMBER[3] | | Y | Y | Y | | Y | | Y | Y | | Not free | ambermd.org |
| Ascalaph Designer | Y | Y | Y | Y | Y | Y | I | Y | Y | Molecular building (DNA, proteins, hydrocarbons, nanotubes).
Molecular dynamics. GPU acceleration. | Free & Commercial | Ascalaph Project |
| Automated Topology Builder (ATB) | | Y | Y | | | | | | | Automated molecular topology building service for small molecules (< 99 atoms). GROMOS, GROMACS, CNS formats with validation
Repository for molecular topologies and pre-equilibrated systems | Free for academic use | Automated Topology Builder |
| Avogadro | Y | Y | Y | | | | I | | | Molecule building, editing (Peptides, small molecules, crystals), Conformational analysis, 2D/3D conversion. Extensible interfaces to other tools. | Free, open source | Avogadro |
| Balloon | | Y | Y | | | | | | | 2D/3D conversion and conformational analysis. | Free to use, closed source | Åbo Akademi |
| BOSS | | | Y | | Y | | Y | | | OPLS | Commercial | Yale University |
| CHARMM | | Y | Y | Y | Y | I | I | Y | | Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) | Not free | charmm.org |
| Chemitorium | Y | Y | | | | | | | | Free 2D/3D graphical organic molecule builder, viewer and visualisation tool. | Free | link |
| ChemSketch | Y | Y | Y | | | | | | | Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified CHARMM for fast stable inaccurate optimization of single molecules up to 1000 atoms | Free | Advanced Chemistry Development, Inc. |
| COSMOS | Y | Y | Y | Y | Y | | I | | | Hybrid QM/MM COSMOS-NMR force field with fast semi-empirical calculation of electrostatic and/or NMR properties. 3-D graphical molecule builder and viewer. | Free (without GUI) and commercial | COSMOS Software |
| Culgi | Y | Y | Y | Y | Y | | | | | Atomistic simulations and mesoscale methods. | Not free | Culgi BV |
| Deneb | Y | Y | I | I | | | I | | | Deneb is a powerful application capable of managing hundreds of projects, each containing hundreds of simulations applied to different samples,every one containing thousands of atoms. Deneb interfaces with most relevant simulation packages (SIESTA, QE, VASP,etc.): Launch your simulation into a remote host with a single click, Deneb will monitor them for you and retrieve the outputs. | Commercial/Trial available | AtelGraphics inc. |
| Desmond | Y | Y | Y | Y | | Y | | | | High Performance MD. Comes with a comprehensive GUI for building, visualizing, and reviewing results as well as calculation setup up and launching. | Free and commercial | D. E. Shaw Research |
| Discovery Studio | Y | Y | Y | Y | Y | | Y | Y | | Discovery Studio is a comprehensive life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Capabilities include, small molecule simulations, QM/MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. | Closed source/Trial available | Accelrys |
| fold.it | Y / I | Y | Y | Y | Y | Y | I | | | University of Washington and The Baker Labs. Structure prediction. Protein folding. | Free, download | fold.it download page |
| FoldX | I | Y | Y | | | | | | | Energy calculations and protein design | Free for academic use | CRG |
| GoVASP | Y | | I | I | | | I | | | GoVASP is a sophisticated graphical user interface for the Vienna Ab-Initio Simulation Package (VASP). GoVASP comprises tools to prepare, perform and monitor VASP calculations and to evaluate and visualize the computed data. | Closed source/Not free/Trial available | Windiks Consulting |
| GPIUTMD | I | I | Y | Y | | I | | | Y | GPIUTMD stands for Graphic Processors at Isfahan University of Technology for Many-particle Dynamics. It performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs to attain a level of performance equivalent to hundreds of processors on a fast cluster. | Closed source/Not free/Demo available | GPIUTMD |
| GROMACS | | | | Y | | Y | | | Y | High performance MD | Free | gromacs.org |
| GROMOS | | | Y | Y | | | | | | Geared towards biomolecules | Not free | GROMOS Homepage |
| GULP | | | Y | Y | | | | | | Molecular dynamics and Lattice optimization | Free for academic use | https://projects.ivec.org/gulp/ |
| HOOMD-blue | | | Y | Y | | | | | Y | General-purpose Molecular Dynamics highly optimized for GPUs. Includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimization, etc... | Free, open source | http://codeblue.umich.edu/hoomd-blue/ index.html |
| ICM | Y | Y | Y | | Y | | I | Y | | Powerful global optimizer in an arbitrary subset of internal variables, NOEs, Protein docking, Ligand docking, Peptide docking, EM, Density placement | Not free | Molsoft |
| LAMMPS | | | Y | Y | Y | Y | I | | Y | Has potentials for soft and solid-state materials and coarse-grain systems | Free | Sandia |
| MacroModel | Y | Y | Y | Y | Y | | I | Y | | OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimization, MD. Includes the Maestro GUI which provides visualization, molecule building, calculation setup, job launching and monitoring, project-level organization of results and access to a suite of other modelling programs. | Commercial | Schrödinger |
| MAPS | Y | Y | Y | Y | Y | | Y | | Y | Building, visualization and analysis tools in a single user interface together with access to multiple simulation engines. | Closed source/Trial available | Scienomics |
| Materials Studio | Y | Y | Y | Y | Y | | Y | Y | Y | Materials Studio is a software environment that brings the materials simulation technology to desktop computing, solving key problems throughout the R&D process. | Closed source/Trial available | Accelrys |
| MedeA | Y | Y | Y | Y | Y | | Y | | | MedeA combines leading experimental databases and major computational programs like the Vienna Ab-Initio Simulation Package (VASP), LAMMPS, GIBBS with sophisticated materials property prediction, analysis, and visualization. | Closed source/Trial available | Materials Design |
| MCCCS Towhee | | | | | Y | | | | | Originally designed for the prediction of fluid phase equilibria | Free | Towhee Project |
| MDynaMix | | | | Y | | | | | | Parallel MD | Free | Stockholm University |
| MOE | Y | Y | Y | Y | | | I | Y | | Molecular Operating Environment | Commercial | Chemical Computing Group |
| MOIL | Y | Y | Y | Y | | | | | | Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling. | Free | link |
| molecools | Y | Y | | | | | | | | Simple Javascript molecular visualization tool | | link |
| MOLDY | | | | Y | | | | | | Parallel, only pair-potentials, Cell lists, modified Beeman's algorithm | Free | Moldy |
| ORAC | | | Y | Y | | Y | | | | A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level | Free, open source | ORAC download page |
| NAB[4] | | Y | | | | | | | | Generation of Models for "Unusual" DNA and RNA | Free | Case group |
| Packmol | | Y | | | | | | | | Builds complex initial configurations for Molecular Dynamics | | link |
| Prime | Y | Y | Y | | Y | | I | Y | | Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized | Commercial | Schrödinger |
| Protein Local Optimization Program | | Y | Y | Y | Y | | | | | Helix, loop, and side chain optimization. Fast energy minimization. | Not free | PLOP wiki |
| p4vasp | Y | Y | | | | | | | | Python-based viewer, structure builder and VASP results browser. Shows band-structure, charge densities and simulates STM images. | Free, open source | p4vasp.at |
| PyMol | Y | Y | | | | | | | | Python-based viewer, many plugins to other software. Some mutagenisis. | Free, open source | PyMol.org |
| QMOL | Y | | | | | | | | | Protein viewer, provided by DNASTAR | Free | DNASTAR, Inc. |
| RasMol | Y | | | | | | | | | Fast viewer | Free | RasMol |
| Raster3D | Y | | | | | | | | | High quality raster images | Free | University of Washington |
| RedMD[5] | I | Y | Y | Y | Y | | | | | Reduced MD. Package for coarse-grained simulations. | Free on GNU Licence | University of Warsaw, ICM |
| StruMM3D (STR3DI32) | Y | Y | Y | Y | ' | | ' | | | Sophisticated 3-D molecule builder and viewer, advanced structural analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking and the handling of complexes. | The 200 atom version is free | Exorga, Inc. |
| Selvita Protein Modeling Platform | Y | Y | Y | | Y | | | | | Protein structure prediction, homology modeling, ab initio modeling, loop modeling, protein threading | Commercial | Selvita Ltd |
| SCIGRESS | Y | Y | Y | Y | | | Y | Y | | MM, DFT, Semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, Virtual screening, Automated builders (molecular dynamics, proteins, crystals) | Commercial | SCIGRESS.com |
| SimBioSys' MoDeST (Molecular Design Software Toolkit) | Y | Y | Y | | | | | | Y | molecular docking, scoring functions for docking, "ligand-based", "fragment-based", "de-novo" | Not Free | SimBioSys Inc. |
| Spartan | Y | Y | Y | | Y | | Y | Y | | Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, spectra, reactivity, and selectivity. | Commercial, Trial Available | Wavefunction, Inc. |
| SwissParam | | | | | | | | | | Web server to determine automatically parameters and topologies for small organic molecules, for use with the CHARMM all atoms force field. Files can be used with CHARMM and GROMACS. | Free for academic. CHARMm licence required for commercial usage. | SwissParam. |
| TeraChem | | | Y | Y | | | Y | | Y | High performance GPU-accelerated ab initio Molecular Dynamics and TD/DFT software package for very large molecular or even nanoscale systems. The software runs on NVIDIA GPUs and 64-bit Linux, and is based on heavily optimized CUDA code. | Closed source / Trial licenses available | PetaChem LLC |
| TINKER | I | Y | Y | Y | Y | | I | Y | | Software tools for molecular design | Free | Washington University |
| Tremolo-X | I | | Y | Y | | | | | | Fast, parallel MD | Not Free | Tremolo-X |
| UCSF Chimera | Y | Y | Y | | | | | | | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | | University of California |
| VEGA ZZ | Y | Y | Y | I | Y | | | Y | Y | 3D viewer, multiple file format support, 2D and 3D editor, surface calculation, conformational analysis, MOPAC and NAMD interfaces, MD trajectory analysis, molecular docking, virtual screening, database engine, parallel design, OpenCL acceleration, etc. | Free for academic use | VEGA ZZ Web site |
| VLifeMDS | Y | Y | Y | | Y | | I | | Y | Complete Molecular Modelling Software, QSAR, Combinetorial Library generation, Pharmacophore, Cheminformatics, docking, etc. | Not free | Vlife Sciences Technologies |
| VMD + NAMD | Y | Y | Y | Y | | Y | | Y | Y | Fast, parallel MD, CUDA | Open source, free to academics | Beckman Institute |
| WHAT IF | Y | Y | I | I | I | | | | | Visualizer for MD. Interface to GROMACS. | Not free | WHAT IF |
| xeo | Y | Y | | | | | | | | open project management for nanostructures | | link |
| YASARA | Y | Y | Y | Y | | | Y | | | Molecular-graphics, -modeling and -simulation program | Not free | YASARA.org |
| Zodiac | Y | Y | Y | | | | | | | Drug design suite | | link |
