MISPR: an open-source package for high-throughput multiscale molecular simulations

Journal Article · Wed Sep 21 00:00:00 EDT 2022 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-022-20009-w· OSTI ID:1904003

Atwi, Rasha ^[1]; Bliss, Matthew ^[1]; Makeev, Maxim ^[1]; Rajput, Nav Nidhi ^[1]

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1. State University of New York (SUNY), Stony Brook, NY (United States)

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

• Research Organization: State University of New York (SUNY), Stony Brook, NY (United States)
• Sponsoring Organization: USDOE Office of Science (SC); LG Energy Solutions; Stony Brook Institute for Advanced Computational Science (iACS); National Science Foundation (NSF)
• Grant/Contract Number: ACI-1548562
• OSTI ID: 1904003
• Journal Information: Scientific Reports, Vol. 12, Issue 1; ISSN 2045-2322
• Publisher: Nature Publishing Group
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
atomistic models
computational chemistry
computational methods
density functional theory
electronic structure
fluids
molecular dynamics