TY - JOUR
T1 - Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE)
AU - Thompson, Matthew W.
AU - Gilmer, Justin B.
AU - Matsumoto, Ray A.
AU - Quach, Co D.
AU - Shamaprasad, Parashara
AU - Yang, Alexander H.
AU - Iacovella, Christopher R.
AU - McCabe, Clare
AU - Cummings, Peter T.
N1 - Funding Information:
The development of MoSDef, as reported in this paper, was primarily supported by the National Science Foundation (NSF) through grant Division of Advancedo Cyberinfrastructure (OAC) OAC-1835874 “Software for Building a Community-Based Molecular Modeling Capability Around the Molecular Simulation Design Framework (MoSDeF).” Earlier developments leading to MoSDeF were supported by previous NSF grants Division of Chemical, Bioengineering, Environmental, and Transport Systems (CBET) CBET-1028374 “Cyber-Enabled Design of Functional Nanomaterials,” OAC-1047828 “Development of an Integrated Molecular Design Environment for Lubrication Systems (iMoDELS)” and OAC-1535150 “Development of a Software Framework for Formalizing Forcefield Atom-Typing for Molecular Simulation.” The development of code within MoSDeF specifically relevant to energy storage systems and the example described in Section 3.2 were supported as part of the Fluid Interface Reactions, Structures and Transport (FIRST) Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. The development of code within MoSDeF specifically relevant to self-assembling lipid systems and the example described in Section 3.3 were supported by National Institute of Arthritis and Musculoskeletal and Skin Diseases grant R01AR072679 “Insights into Skin Barrier Function: In Silico and Experimental Studies of Healthy and Diseased Stratum Corneum Lipid Models.” We acknowledge key contributions to MoSDeF by former group members Christoph Klein (myriad.com) and Andrew Z. Summers (enthought.com) and by ISIS staff Peter Volgesi, Umesh Timalsina, and Janos Sallai.
Publisher Copyright:
© 2020, © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
PY - 2020/6
Y1 - 2020/6
N2 - 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.
AB - 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.
KW - Molecular dynamics
KW - Monte Carlo simulation
KW - open-source
KW - reproducibility
UR - http://www.scopus.com/inward/record.url?scp=85083846232&partnerID=8YFLogxK
U2 - 10.1080/00268976.2020.1742938
DO - 10.1080/00268976.2020.1742938
M3 - Article
AN - SCOPUS:85083846232
SN - 0026-8976
VL - 118
JO - Molecular Physics
JF - Molecular Physics
IS - 9-10
M1 - e1742938
ER -