MDverse, shedding light on the dark matter of molecular dynamics simulations
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD — data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
Authors
- Erik Lindahl (ORCID: https://orcid.org/0000-0002-2734-2794)
- Rebecca J. Howard (ORCID: https://orcid.org/0000-0003-2049-3378)
- Marc Baaden (ORCID: https://orcid.org/0000-0001-6472-0486)
- Kresten Lindorff‐Larsen (ORCID: https://orcid.org/0000-0002-4750-6039)
- Johanna K. S. Tiemann (ORCID: https://orcid.org/0000-0001-7551-6245)
- Lucie Delemotte (ORCID: https://orcid.org/0000-0002-0828-3899)
- Mohamed Oussaren
- Magdalena Szczuka (ORCID: https://orcid.org/0009-0001-8044-540X)
- Pierre Poulain (ORCID: https://orcid.org/0000-0003-4177-3619)
- Steven Garcia (ORCID: https://orcid.org/0009-0000-1155-930X)
- Matthieu Chavent (ORCID: https://orcid.org/0000-0003-4524-4773)
- Lisa Bouarroudj (ORCID: https://orcid.org/0009-0001-1177-7873)
Institutions
- University of Copenhagen (DK)
- Centre National de la Recherche Scientifique (FR)
- Stockholm University (SE)
- Université Fédérale de Toulouse Midi-Pyrénées (FR)
- Université Paris Cité (FR)
- Science for Life Laboratory (SE)
- Laboratoire de Biochimie Théorique (FR)
- Institut de Pharmacologie et de Biologie Structurale (FR)
- Institut Jacques Monod (FR)
- KTH Royal Institute of Technology (SE)
Publication Details
- Journal
- eLife
- Published
- 2024-08-30
- DOI
- https://doi.org/10.7554/elife.90061.3
- Citations
- 13
- Primary Topic
- Scientific Computing and Data Management
- Type
- article
- Field-Weighted Citation Impact
- 13.66
Funders
- Novo Nordisk Fonden