Simulation Foundry: Automated and F.A.I.R. Molecular Modeling

Abstract:

The Simulation Foundry (SF) is a modular workflow for the automated creation of molecular modeling (MM) data. MM allows for the reliable prediction of the microscopic and macroscopic properties of multicomponent systems from first principles. The SF makes MM repeatable, replicable, and findable, accessible, interoperable, and reusable (F.A.I.R.). The SF uses a standardized data structure and file naming convention, allowing for replication on different supercomputers and re-entrancy. We focus on keeping the SF simple by basing it on scripting languages that are widely used by the MM community (bash, Python) and making it reusable and re-editable. The SF was developed to assist expert users in performing parameter studies of multicomponent systems by high throughput molecular dynamics simulations. The usability of the SF is demonstrated by simulations of thermophysical properties of binary mixtures. A standardized data exchange format enables the integration of simulated data with data from experiments. The SF also provides a complete documentation of how the results were obtained, thus assigning provenance. Increasing computational power facilitates the intensification of the simulation process and requires automation and modularity. The SF provides a community platform on which to integrate new methods and create data that is reproducible and transparent (https://fairdomhub.org/studies/639/snapshots/1, https://fairdomhub.org/studies/639/snapshots/2).

SEEK ID: https://fairdomhub.org/publications/624

DOI: 10.1021/acs.jcim.0c00018

Projects: Simulation Foundries

Publication type: Journal

Journal: Journal of Chemical Information and Modeling

Citation: J. Chem. Inf. Model. 60(4):1922-1927

Date Published: 27th Apr 2020

Registered Mode: by DOI

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Citation
Gygli, G., & Pleiss, J. (2020). Simulation Foundry: Automated and F.A.I.R. Molecular Modeling. In Journal of Chemical Information and Modeling (Vol. 60, Issue 4, pp. 1922–1927). American Chemical Society (ACS). https://doi.org/10.1021/acs.jcim.0c00018
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Created: 8th Oct 2021 at 15:17

Last updated: 8th Oct 2021 at 15:17

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