Molecular Design Toolkit

Seamlessly integrated molecular simulation, visualization and cloud computing


Autodesk’s Molecular Design Toolkit is a free and open environment to design, simulate, visualize, and interact with molecular systems. It enables design at the atomic level with a suite of open source molecular modeling tools and seamless access to cloud computing. 

Introduction Video


Energy models calculate molecular properties: potential energy, forces, etc.

Models include:

  • Forcefields: Amber, GAFF, CHARMM*
  • Ab Initio Methods: RHF, DFT, MP2, CASSCF
  • Semiempirical methods: AM1*, PM3*, DFTB*
  • Toy models: Harmonic Oscillators, Tully multistate models

Using implementations from OpenMM, PySCF and SQM


An Integrator moves a molecule forward in time based on forces.

Models include:

  • Langevin dynamics (NVT, NPT*)
  • Velocity Verlet (NVE)
  • Surface Hopping*

Using implementations from OpenMM and custom python codes


MDT exposes ready-to-analyze structural and calculation data for various objects, including:


  • Atoms, bond topology, primary structure
  • Position and momenta
  • Calculated properties (potential energy, forces, dipole moments, partial charges, etc.)

Electronic wavefunctions:

  • Basis set data
  • Molecular orbitals
  • Overlap, Fock, and Hamiltonian matrices
  • CI Vectors


  • Time series - coordinates and properties
  • Geometric analysis methods (for analyzing time evolution of angles, RMSDs, etc.)


  • Build 3D structures from SMILES, IUPAC names, PDB assemblies, even DNA sequences
  • Read and write files from SDF, PDB, XYZ, mmCIF, ...
  • Measure and adjust cartesian geometry and internal coordinates
  • Add missing atoms
  • Measure and adjust cartesian geometry and internal coordinates
  • Fix protonation, hybridization and formal charges
  • Assign forcefields to biomolecules
  • Parameterize small molecules
  • Solvate crystal stuctures*

*In development for version 0.8


Simultaneous 2D and 3D drawings with cross-representation selections.


Single-point and trajectory orbital visualization.


Automatically generated user interfaces to configure simulation methods.


Click to select atoms or amino acids, and use the results in a script.


The Molecular Design Toolkit is an integrated, self-contained environment for computational chemistry - you can start running molecular dynamics, electronic structure, interactive visualizations, and distributed simulations as soon as it's installed. 


An intuitive Python API gives you access to mature, research-level software. Run one job on your laptop or 10,000 jobs in the cloud using a science-focused, open source job scheduling system.


MDT is free, open source, and ready for use by the scientific community. It uses open, platform-independent technologies like Python, Jupyter, Docker, and WebGL, together with powerful scientific open source software, including OpenMM, AmberTools, OpenBabel, and many more.


Where did the Molecular Design Toolkit come from?

The Molecular Design Toolkit was created by the BioNano Research group at Autodesk, which works to push the frontiers of computer-aided design towards the nanoscale. Learn more about us.

The toolkit is being maintained as an open-source, community-driven project on GitHub, and embodies the contributions of many scientists, both from its open source components and from code contributions.

Do I need to know python?

Yes - the Molecular Design Toolkit is a Python library that can be used in Python scripts and notebooks.

Although familiarity with the notebook environment is helpful, you don't need to be a programming expert. Check out the tutorials and example notebooks to get you up and running.

These resources can help you get started with Python and/or the Jupyter notebook environment:

What other scientific software does the toolkit use?

Rather than reinvent the wheel, MDT has been built using mature scientific open source packages. Here are some of the projects MDT that MDT integrates to provide its functionality.

Scientific modeling:


BioNano projects:

Is it really free?

Yes! The software is free, and open source, and has been released under the Apache 2.0 license, meaning you're free to use it, distribute it, modify it, and patent any discoveries arising from its use. 

Where do my jobs run?

Many of MDT's functions require a Docker server to run. The toolkit comes preconfigured to use a free but limited limited demo cloud computing server - an internet connection is required.

Can I use the cloud backend outside of the toolkit?

The cloud computing infrastructure is installable as a standalone NPM package.

How can I help?

The toolkit is a project from Autodesk Research. We are working with members of an enthusiastic and growing community - and hopefully you! Contributions can take many forms, from filing bug reports to discussing computational techniques to providing feedback to contributing to the code.

What's next?

The initial version offers bare bones quantum chemistry and molecular mechanics, but we're constantly adding scientific features. Short-term priorities include:

  • free energy perturbation
  • excited state dynamics
  • GPU acceleration

We want to hear from you! What are your use cases? What kinds of chemistry do you want to do in a notebook?


    Aaron Virshup. Pr. Research Scientist

    Before coming to Autodesk, Aaron studied biological quantum dynamics at the University of Illinois at Urbana-Champaign and physics-based molecular design techniques at Duke University. With his background in computational physics, molecular simulation, and chemical design, Aaron works to enable a future of designing materials, chemicals, and processes at the atomic level. 

    Dion Amage. Sr. Software Engineer

    Dion Amago Whitehead finished a post-doc in Münster, Germany before heading off to the shiny worlds of mobile games in San Francisco. After learning how to build scalable systems and nice user experiences, he is applying that knowledge to create powerful, easy to use scientific tools.

    Justin McCandless. Sr. Software Engineer

    Justin studied electrical engineering at the University of Michigan before joining several startups in the US (and one in China). Now he works on the Molecular Design Toolkit project with an interest in graphics and open source.

    Malte Tinnus. Sr. Pr. Designer

    Malte is a versatile designer specialized in 3D design and interactions. He is collaborating with leading scientists to envision the paradigms and tools needed to exploit the intersection of design and life.

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