Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework
Authors:
Peter T. Cummings1, Clare McCabe1,2, Christopher R. Iacovella1, Akos Ledeczi3, Eric Jankowski4, Arthi Jayaraman5, Jeremy C. Palmer6, Edward J. Maginn7, Sharon C. Glotzer8, Joshua A. Anderson8, J. Ilja Siepmann9,10, Jeffrey Potoff11, Raymond A. Matsumoto1, Justin B. Gilmer12, Ryan S. DeFever7, Ramanish Singh9,10, Brad Crawford11
Affiliations
  1. Department of Chemical and Biomolecular Engineering and Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN
  2. Department of Chemistry, Vanderbilt University, Nashville, TN
  3. Department of Electrical Engineering and Computer Science and Institute for Software Integrated Systems, Vanderbilt University, Nashville, TN
  4. Micron School of Materials Science and Engineering, Boise State University, Boise, ID
  5. Departments of Chemical and Biomolecular Engineering and of Materials Science and Engineering, University of Delaware, Newark, DE
  6. Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
  7. Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN
  8. Departments of Chemical Engineering, of Materials Science, and of Physics, University of Michigan, Ann Arbor, MI
  9. Department of Chemistry and Chemical Theory Center, University of Minnesota
  10. Department of Chemical Engineering and Materials Science, University of Minnesota, MN
  11. Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI
  12. Interdisciplinary Graduate Program in Materials Science and Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN
Abstract
Molecular simulation has emerged as an important sub-field of chemical engineering, due in no small part to the leadership of Keith Gubbins. A characteristic of the chemical engineering molecular simulation community is the commitment to freely share simulation codes and other key software components required to perform a molecular simulation under open-source licenses and distribution on public repositories such as GitHub. Here we provide an overview of open-source molecular modeling software in Chemical Engineering, with focus on the Molecular Simulation Design Framework (MoSDeF). MoSDeF is an open-source Python software stack that enables facile use of multiple open-source molecular simulation engines, while at the same time ensuring maximum reproducibility.
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