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
- Department of Chemical and Biomolecular Engineering and Multiscale
Modeling and Simulation Center, Vanderbilt University, Nashville, TN
- Department of Chemistry, Vanderbilt University, Nashville, TN
- Department of Electrical Engineering and Computer Science and
Institute for Software Integrated Systems, Vanderbilt University,
Nashville, TN
- Micron School of Materials Science and Engineering, Boise State
University, Boise, ID
- Departments of Chemical and Biomolecular Engineering and of Materials
Science and Engineering, University of Delaware, Newark, DE
- Department of Chemical and Biomolecular Engineering, University of
Houston, Houston, TX
- Department of Chemical and Biomolecular Engineering, University of
Notre Dame, Notre Dame, IN
- Departments of Chemical Engineering, of Materials Science, and of
Physics, University of Michigan, Ann Arbor, MI
- Department of Chemistry and Chemical Theory Center, University of
Minnesota
- Department of Chemical Engineering and Materials Science, University
of Minnesota, MN
- Department of Chemical Engineering and Materials Science, Wayne State
University, Detroit, MI
- 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.
TOC graphic