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mBuild

A hierarchical, component based molecule builder

With just a few lines of mBuild code, you can assemble reusable components into complex molecular systems for molecular simulations.

  • mBuild is designed to minimize or even eliminate the need to explicitly translate and orient components when building systems: you simply tell it to connect two pieces!
  • mBuild keeps track of the system's topology so you don't have to worry about manually defining bonds when constructing chemically bonded structures from smaller components.

mBuild is a part of the MoSDeF ecosystem

The mBuild software, in conjunction with the other Molecular Simulation Design Framework (MoSDeF) tools, supports a wide range of simulation engines, including Cassandra, GPU Optimized Monte Carlo (GOMC), GROMACS, HOOMD-blue, and Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The mBuild and MoSDeF tools allow simulation reproducibility across the various simulation engines, eliminating the need to be an expert user in all the engines to replicate, continue, or advance the existing research. Additionally, the software can auto-generate many different systems, allowing large-scale screening of chemicals and materials using Signac to manage the simulations and data.

The MoSDeF software is comprised the following packages:
  • mBuild -- A hierarchical, component based molecule builder
  • foyer -- A package for atom-typing as well as applying and disseminating forcefields
  • GMSO -- Flexible storage of chemical topology for molecular simulation
.. toctree::
        :caption: Getting Started
        :maxdepth: 2

        getting_started/example_system
        getting_started/installation/installation_toc
        getting_started/quick_start/quick_start
        getting_started/writers/writers
        getting_started/tutorials/tutorials


.. toctree::
        :caption: Topic Guides
        :maxdepth: 2

        topic_guides/recipe_development
        topic_guides/data_structures
        topic_guides/load_data
        topic_guides/coordinate_transforms
        topic_guides/recipes


.. toctree::
        :caption: Reference
        :maxdepth: 2

        reference/units
        reference/citing_mbuild
        reference/older_documentation