Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE)

Matthew W. Thompson, Justin B. Gilmer, Ray A. Matsumoto, Co D. Quach, Parashara Shamaprasad, Alexander H. Yang, Christopher R. Iacovella, Clare McCabe, Peter T. Cummings*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

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 reproducibilitya. 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.

Original languageEnglish
Article numbere1742938
JournalMolecular Physics
Volume118
Issue number9-10
Early online date8 Apr 2020
DOIs
Publication statusPublished - Jun 2020

Keywords

  • Molecular dynamics
  • Monte Carlo simulation
  • open-source
  • reproducibility

ASJC Scopus subject areas

  • Biophysics
  • Molecular Biology
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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