MDverse, shedding light on the dark matter of molecular dynamics simulations.

ABSTRACT: 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 identif

SUBMITTER: Tiemann JKS 

PROVIDER: S-EPMC11364437 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature