• Modelling and Simulation

    This is a list of computer programs that are predominantly used for molecular mechanics calculations.

    Biomolecular simulations, protein folding. Free

    From Acellera Ltd, Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA. Basic version free. Commercial version available.

    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 (licensed under GNU GPL)
    Not free

    Molecular building (DNA, proteins, hydrocarbons, nanotu
    Molecular dynamics. GPU acceleration.
    Free (GNU GPL) & Commercial


    Ascalaph Project
    Automated Topology Builder (ATB)
    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

    Molecule building, editing (Peptides, small molecules, crystals), Conformational analysis, 2D/3D conversion. Extensible interfaces to other tools.
    Free (GNU GPL)
    Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm)
    Not free

    Chemical reaction kintetics.
    Not free
    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< CP2K
    CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems.
    Free (GNU GPLv2 or later)< Culgi
    Atomistic simulations and mesoscale methods.
    Not free
    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
    Discovery Studio
    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
    University of Washington and The Baker Labs. Structure prediction. Protein folding.
    Free, download< FoldX
    Energy calculations and protein design
    Free for academic use
    performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs.
    Closed Source
    High performance MD
    Free (GNU GPLv2)
    Geared towards biomolecules
    Not free
    Molecular dynamics and Lattice optimization
    Free for academic use
    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< ICM
    Powerful global optimizer in an arbitrary subset of internal variables, NOEs, Protein docking, Ligand docking, Peptide docking, EM, Density placement
    Not free< LAMMPS
    Has potentials for soft and solid-state materials and coarse-grain systems
    Free, Open Source. (GNU GPLv2)< MacroModel
    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< MAPS
    Building, visualization and analysis tools in a single user interface together with access to multiple simulation engines.
    Closed source/Trial available< Materials Studio
    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< MCCCS Towhee
    Originally designed for the prediction of fluid phase equilibria
    Free< MDynaMix
    Parallel MD
    Free< MedeA
    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< MOE
    Molecular Operating Environment
    Commercial< MOIL
    Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling.
    Free< NAB[5]
    Generation of Models for “Unusual” DNA and RNA
    Free< NAMD + VMD
    Fast, parallel MD, CUDA
    Open source, free to academics< NWChem
    High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM/MM methods
    Open-source, Educational Community License version 2.0< ORAC
    A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level
    Free, open source< Packmol
    Builds complex initial configurations for Molecular Dynamics
    Free, Open Source. (GNU GPL)< Prime
    Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized
    Commercial< Protein Local Optimization Program
    Helix, loop, and side chain optimization. Fast energy minimization.
    Not free< Q
    (I) Free Energy Perturbation (FEP) simulations. (II) Empirical Valence Bond (EVB) calculations of reaction free energies. (III) Linear Interaction Energy (LIE) calculations of receptor-ligand binding affinities.
    Uppsala Molekylmekaniska HB< RedMD[6]
    Reduced MD. Package for coarse-grained simulations.
    Free on GNU Licence< SCIGRESS
    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< Spartan
    Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, spectra, reactivity, and selectivity.
    Commercial, Trial Available< StruMM3D (STR3DI32)
    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< TeraChem
    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< TINKER
    Software tools for molecular design
    Free< Tremolo-X
    Fast, parallel MD
    Not Free< UCSF Chimera
    Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development.
    University of California
    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
    Complete Molecular Modelling Software, QSAR, Combinetorial Library generation, Pharmacophore, Cheminformatics, docking, etc.
    Not free
    Vlife Sciences Technologies
    Visualizer for MD. Interface to GROMACS.
    Not free

    YASARA Molecular-graphics, -modeling and -simulation program
    Not free

    Agile Molecule G, MB  

    AMBER MM, MD  

    AMPAC QM  

    AMSOL QM  

    APEX-3D DD  

    AutoDock DD  

    Babel U  

    CAChe MP, P  

    Cambridge Structural Database (CSD) DB  


    CHARMm MM, MD  


    Chem-X MP, DD, P xxx  

    ChemDBS-3D DD, DB xxx  

    CHIME G, P  

    ClogP DD, P  

    CMR DD  

    CLIP DD  

    Composer BP, MB  

    CONCORD MB xxx  

    CS ChemOffice Pro MP, P  

    DGEOM 95 MB  

    DGII MB xxx  

    DMol QM  

    DOCK DD  

    DSSP BP, DB  

    EGO MD  



    GASP DD  

    Gaussian QM  

    GEMM G, BP xxx  

    GERM DD xxx  

    GLARE DD, P, U xxx  

    gOpenMol G  

    GRAMM BP, P  

    GRASP G  



    HASL DD  

    hBar Lab QM  


    HINT DD  

    HONDO QM xxx  

    HyperChem MP, P  

    ICM BP, MM, MC  

    Iditis BP, DB  

    Insight II MP  

    ISIS DB, P  

    Jaguar QM  

    Leapfrog DD  


    Look/GeneMine BP, MB  

    Loopy MB, BI  

    Ludi DD  

    MacMolecule/PCMolecule G, P  

    MacroModel MP  

    MAGE G, P  

    Match xxx  

    MC-SYM BP  

    MidasPlus G, BP  

    MM3 xxx  


    Moil MD  

    Moil-View G  

    Molconn-z DD  


    MOLGEN+ P  

    MolScript G  


    MOPAC 93 QM, P  

    NAB BP  

    NAMD MD  

    NAMOT BP  

    NanoVision G, BP, P  

    NAOMI BP  

    NEST MB, BI  

    NT-NMRPipe BP  

    “O” X, G  

    PDBTool BP  

    PKalc DD, P  

    PovChem G  

    PQS: Parallel Quantum Solutions QM,MM  

    Profix BI  

    PrologD DD, P  

    PrologP DD, P  


    Protein Data Bank (PDB) DB, BP  


    QUEST DB  

    RasMol G, P  

    Raster3D G  

    Ribbons G, BP  

    SCAP MB, BI  



    Setor G xxx  

    Spartan QM  


    SYBYL MP  

    UHBD MM  

    UniChem QM  

    Vega G,P,U  

    Visual Molecular Dynamics (VMD) – 32 and 64 bit versions available G, MD  

    WebLab G, P  

    What If BP  

    XMol G  

    X-PLOR X  

    XtalView X  

    ZINDO QM xxx  

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