ArticleMolecular physics2020
Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE).
Article in Molecular physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations.Journal of chemical information and modeling · 2026Article
- Bayesian Modeling of Polarizable Water: Lessons for Force Field Development.Journal of chemical theory and computation · 2026Article
- Multiscale simulation of stratum corneum lipid mixtures: effects of ceramide headgroups on structural organization and hydrogen bonding networks.International journal of pharmaceutics · 2026Article
- New Coarse-Grained Models for Stratum Corneum Ceramides Reveal Headgroup-Dependent Structural Organization.The journal of physical chemistry. B · 2025Article
- Atomistic Polymer Modeling: Recent Advances and Challenges in Building and Parametrization Workflows.Macromolecules · 2025Review
- SEAMM: A Simulation Environment for Atomistic and Molecular Modeling.The journal of physical chemistry. A · 2025Article
- Achieving Reproducibility and Replicability of Molecular Dynamics and Monte Carlo Simulations Using the Molecular Simulation Design Framework (MoSDeF).Journal of chemical and engineering data · 2025Review
- Validating Structural Predictions of Conjugated Macromolecules in Espaloma-Enabled Reproducible Workflows.International journal of molecular sciences · 2025Article
- The Sphingosine and Phytosphingosine Ceramide Ratio in Lipid Models Forming the Short Periodicity Phase: An Experimental and Molecular Simulation Study.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.PLoS computational biology · 2024Article
- Data scheme and data format for transferable force fields for molecular simulation.Scientific data · 2023Article
- Generative Models as an Emerging Paradigm in the Chemical Sciences.Journal of the American Chemical Society · 2023Review
- Using molecular simulation to understand the skin barrier.Progress in lipid research · 2022Review
- Article
- py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.Journal of chemical theory and computation · 2022Article
- Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition.Langmuir : the ACS journal of surfaces and colloids · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.