MSIBI: Multi-state Iterative Boltzmann Inversion

MSIBI is a Python package that implements the Multi-state Iterative Boltzmann Inversion (MS-IBI) method for coarse-graining in molecular dynamics.

This implementation provides an intuitive Python API for running iterative Boltzmann inversion (IBI) across multiple states (MS-IBI) or a single state. It is designed to make it easy to chain together multiple optimization runs—for example, you can first optimize a coarse-grained bond-stretching interaction, then hold it fixed while optimizing other interactions like bond bending or non-bonded pair potentials.

MSIBI uses the HOOMD-blue simulation engine under the hood for coarse-grained simulations; however, it does not require that the target (atomistic) simulations are also performed with HOOMD-blue. The resulting coarse-grained potentials are exported in a tabulated format compatible with other simulation engines such as LAMMPS and GROMACS.

Quick start

Python API

Resources

Citation

If you use this package, please cite the following papers. The BibTeX references are:

This paper discusses the design and implementation of MSIBI

@article{Moore2014,
      author = "Moore, Timothy C. and Iacovella, Christopher R. and McCabe, Clare",
      title = "Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion",
      journal = "The Journal of Chemical Physics",
      year = "2014",
      volume = "140",
      number = "22",
      doi = "http://dx.doi.org/10.1063/1.4880555"
}

This paper discusses this python package that implements the MSIBI method

@article{Jones2026,
    doi={10.21105/joss.09244},
    url={https://doi.org/10.21105/joss.09244},
    year={2026},
    publisher={The Open Journal},
    volume={11},
    number={119},
    pages={9244},
    author={Jones, Chris D. and Almarashi, Mazin and Albooyeh, Marjan and Jankowski, Eric and McCabe, Clare},
    title={msibi: Multistate Iterative Boltzmann Inversion}, journal = {Journal of Open Source Software}
}

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