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SEAMM: A Simulation Environment for Atomistic and Molecular Modeling.

Paul Saxe1,2, Jessica Nash1,2, Mohammad Mostafanejad1,2

  • 1Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

The Journal of Physical Chemistry. A
|July 18, 2025
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Summary
This summary is machine-generated.

The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software that simplifies complex molecular simulations. It enhances collaboration and reproducibility in computational molecular science research.

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Area of Science:

  • Computational molecular science
  • Materials science
  • Chemical engineering

Background:

  • Molecular and materials simulations are crucial for scientific discovery but often require specialized expertise.
  • Interoperability between diverse simulation codes remains a challenge, hindering complex problem-solving.

Purpose of the Study:

  • To introduce the Simulation Environment for Atomistic and Molecular Modeling (SEAMM) as a solution for simplifying and integrating molecular simulations.
  • To enhance productivity, collaboration, and reproducibility in computational molecular science research.

Main Methods:

  • SEAMM provides an open-source Python-based graphical user interface for setting up, executing, and analyzing simulations.
  • Workflows are visualized as shareable and reproducible flowcharts.
  • Results and metadata are stored in a datastore accessible via a browser-based dashboard.

Main Results:

  • SEAMM successfully demonstrated flexibility and productivity through diverse examples, including molecular dynamics, quantum code applications, and industrial battery material research.
  • The software facilitates the interoperability of various simulation tools.
  • Reproducibility and transparency in research are significantly improved.

Conclusions:

  • SEAMM is a powerful tool that lowers the barrier to entry for complex simulations.
  • It fosters collaboration and ensures the integrity of scientific research through enhanced reproducibility and transparency.