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Thompson MW, Gilmer JB, Matsumoto RA, Quach CD, Shamaprasad P, Yang AH, Iacovella CR, Cabe CM, Cummings PT. Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE). Mol Phys 2020; 118:e1742938. [PMID: 33100401 PMCID: PMC7576934 DOI: 10.1080/00268976.2020.1742938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 10/24/2022]
Abstract
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a "bespoke" fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibility. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations.
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Affiliation(s)
- Matthew W Thompson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Justin B Gilmer
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Ray A Matsumoto
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Co D Quach
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Parashara Shamaprasad
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Alexander H Yang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Clare M Cabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
| | - Peter T Cummings
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, TN, USA
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Haley JD, Iacovella CR, Cummings PT, McCabe C. Examining the aggregation behavior of polymer grafted nanoparticles using molecular simulation and theory. J Chem Phys 2015; 143:054904. [DOI: 10.1063/1.4927819] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jessica D. Haley
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Christopher R. Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Peter T. Cummings
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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