  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.
