Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application

Meletiou, Athina; Gebbie-Rayet, James; Laughton, Charles

Abstract

The configuration of most current academic high-performance computing (HPC) resources tends to enforce ways of working with, and thinking about, molecular dynamics (MD) simulations that are not always optimal. For example, when the aim of the simulation(s) is to produce a representative sample of a Boltzmann weighted ensemble, the ideal scenario would be to be able to do just that—i.e. to tap into a running simulation of indefinite length, collect data from it in real time, and only terminate the simulation once the quality of a sample was assured. Current approaches, based on batch jobs of proscribed maximum length, and a postprocessing style of data analysis, inhibit this. In the spirit of the Internet of Things, we have developed Tios, a Python application that turns MD simulations into remotely discoverable and accessible streaming web applications to which researchers can connect and download data as they please. Tios is freely available, works with standard MD codes, and requires no modifications to them. In this paper we outline how Tios works and present a number of test cases that demonstrate its capabilities.

Citation

Meletiou, A., Gebbie-Rayet, J., & Laughton, C. (2019). Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application. Journal of Chemical Information and Modeling, 59(8), 3359-3364. https://doi.org/10.1021/acs.jcim.9b00351

• Journal Article Type: Article
• Acceptance Date: Jul 24, 2019
• Online Publication Date: Aug 12, 2019
• Publication Date: Aug 12, 2019
• Deposit Date: Aug 30, 2019
• Publicly Available Date: Aug 13, 2020
• Journal: Journal of Chemical Information and Modeling
• Print ISSN: 1549-9596
• Electronic ISSN: 1549-960X
• Publisher: American Chemical Society
• Peer Reviewed: Peer Reviewed
• Volume: 59
• Issue: 8
• Pages: 3359-3364
• DOI: https://doi.org/10.1021/acs.jcim.9b00351
• Keywords: General Chemistry; General Chemical Engineering; Library and Information Sciences; Computer Science Applications
• Public URL: https://nottingham-repository.worktribe.com/output/2470479
• Publisher URL: http://pubs.acs.org/doi/10.1021/acs.jcim.9b00351
• Additional Information: This document is the Accepted Manuscript version of a Published work that appeared in final form in ACS Journal of Chemical Information and Modeling, copyright ©2019 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jcim.9b00351
• Contract Date: Aug 30, 2019