Simulation studies of molecules primarily produce data that represent the config- uration of the system as a function of the progress variable, usually time. Because of the high-dimensional nature of these data, which grows very quickly, compromises are often necessary and achieved by storing only a subset of the system’s components, for example stripping solvent, and by restricting the time resolution to a scale signif- icantly coarser than the basic timestep of the simulation. The resultant trajectories thus describe the essentially stochastic evolution of molecules of interest. Maintaining their interpretability through metadata is of interest not only because they can aid re- searchers interested in specific systems, but also for reproducibility studies and model refinement. Here, we introduce a standard for the storage of data created by molecular simulations that improves compliance with the FAIR (for Findable, Accessible, Inter- operable, Reusable) principles. We describe a solution conceived in PostgreSQL, along with reference implementations, that provides stringent links between metadata and raw data, which is a major weakness of the established file formats used for storing these data. A possible structure for the logic of SQL queries is included along with salient performance testing. To close, we suggest that a PostgreSQL-based storage of simulation data, in particular when coupled to a visual user interface, can improve the FAIR compliance of molecular simulation data at all levels of visibility, and a prototype solution for accomplishing this is presented.
BT - Journal of Chemical Information and Modeling C1 - 0309 DO - 10.1021/acs.jcim.4c01301 IS - 5 J2 - J. Chem. Inf. Model. LA - eng M3 - Research Article N2 -Simulation studies of molecules primarily produce data that represent the config- uration of the system as a function of the progress variable, usually time. Because of the high-dimensional nature of these data, which grows very quickly, compromises are often necessary and achieved by storing only a subset of the system’s components, for example stripping solvent, and by restricting the time resolution to a scale signif- icantly coarser than the basic timestep of the simulation. The resultant trajectories thus describe the essentially stochastic evolution of molecules of interest. Maintaining their interpretability through metadata is of interest not only because they can aid re- searchers interested in specific systems, but also for reproducibility studies and model refinement. Here, we introduce a standard for the storage of data created by molecular simulations that improves compliance with the FAIR (for Findable, Accessible, Inter- operable, Reusable) principles. We describe a solution conceived in PostgreSQL, along with reference implementations, that provides stringent links between metadata and raw data, which is a major weakness of the established file formats used for storing these data. A possible structure for the logic of SQL queries is included along with salient performance testing. To close, we suggest that a PostgreSQL-based storage of simulation data, in particular when coupled to a visual user interface, can improve the FAIR compliance of molecular simulation data at all levels of visibility, and a prototype solution for accomplishing this is presented.
PY - 2025 SP - 2443 EP - 2455 T2 - Journal of Chemical Information and Modeling TI - A FAIR-compliant management solution for molecular simulation trajectories VL - 65 ER -