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

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.

Contributions of Molecular Dynamics Simulations to Elastohydrodynamic Lubrication

“…This study by Jadhao and Robbins [24] was a significant breakthrough and was highlighted as a key study in our 2018 reviews on both SATA [27] and NEMD simulations [6] in tribology. Moreover, the authors made their large atomic/ molecular massively parallel simulator (LAMMPS) [28] input files publically available in the Supporting Information, ensuring that their results were transparent, reproducible, usable by others, and extensible (TRUE) [29].…”

Open‐source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework

“…Moreover, the SI contains all the instructions needed for the reader to download and run all the utilities and codes needed to reproduce the reported calculations exactly, hence qualifying these as TRUE simulations. 24…”

“…That is, MoSDeF tools enable the initialization, simulation, and analysis workflows of entire scientific studies to be defined in Python scripts. Performing a simulation using MoSDeF, combined with dissemination of simulation scripts on a service such as Github, enables a molecular simulation to be published as a TRUE (transparent, reproducible, usable by others, and extensible) simulation 24 …”

Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework

“…This also allows the framework to be more easily modified, tested, extended, and have fewer bugs than a monolithic approach. Performing a simulation using MoSDeF, combined with dissemination of simulation scripts on a service such as Github, enables a molecular simulation to be published as a TRUE (t ransparent,r eproducible, u sable by others, and e xtensible) simulation 33 .…”

“…Moreover, the SI contains all the instructions needed for the reader to download and run all the utilities and codes needed to reproduce the reported calculations exactly, hence qualifying these as TRUE simulations. 33…”