flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics

flowerMD is a modular “wrapper” package for molecular dynamics (MD) simulation pipeline development, designed to enable fast, reproducible, end-to- end simulation workflows with minimal user effort. An object-oriented design makes flowerMD extensible and highly flexible. This is bolstered by a library-based approach to system initialization, making flowerMD agnostic to system identity, forcefield, and thermodynamic ensemble, and allowing for growth on an as-needed basis.

Why flowerMD?

flowerMD consolidates and automates end-to-end workflows for modeling complex engineering processes, with a focus on emulating physical experiments on organic materials. Following the principals of Transparent, Reproducible, Usable by others, and Extensible TRUE software design, the modular design of flowerMD facilitates building and running workflows for specific materials science research applications, while reducing the cognitive load and programming demands on the user’s part. flowerMD addresses a longstanding need in moelcular dynamics simulation workflow building: reproducible and low-complexity recipes for specifying research workflows, agnostic to specific system identity.

In particular, flowerMD bridges the gaps between the steps of specifying molecules, parametrizing and applying force fields, and launching simulations into one seamless workflow, while remaining flexible enough to change any individual step without necessitating changes elsewhere in the workflow. The recipe-book-style approach of flowerMD reduces the amount of work needed to implement otherwise similar simulations with different molecular species, different molecular representations (i.e. coarse vs fine-grained), different force fields, or different state points.

Quick start

Resources

Citation

If you use flowerMD in your research, please cite the following paper:

Albooyeh, M., Jones, C., Barrett, R., & Jankowski, E. (2023). FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics. Journal of Open Source Software, 8(92), 5989, https://doi.org/10.21105/joss.05989

Python API

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