ACS Publications. Most Trusted. Most Cited. Most Read
ParAMS: Parameter Optimization for Atomistic and Molecular Simulations
My Activity

Figure 1Loading Img
    Application Note

    ParAMS: Parameter Optimization for Atomistic and Molecular Simulations
    Click to copy article linkArticle link copied!

    Other Access OptionsSupporting Information (1)

    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2021, 61, 8, 3737–3743
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jcim.1c00333
    Published May 13, 2021
    Copyright © 2021 American Chemical Society

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    This work introduces ParAMS—a versatile Python package that aims to make parametrization workflows in computational chemistry and physics more accessible, transparent, and reproducible. We demonstrate how ParAMS facilitates the parameter optimization for potential energy surface (PES) models, which can otherwise be a tedious specialist task. Because of the package’s modular structure, various functionality can be easily combined to implement a diversity of parameter optimization protocols. For example, the choice of PES model and the parameter optimization algorithm can be selected independently. An illustration of ParAMS’ strengths is provided in two case studies: (i) a density functional-based tight binding (DFTB) repulsive potential for the inorganic ionic crystal ZnO and (ii) a ReaxFF force field for the simulation of organic disulfides.

    Copyright © 2021 American Chemical Society

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    Supporting Information

    Click to copy section linkSection link copied!

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jcim.1c00333.

    • Mathematical description of the optimization problem, summary of reference data published by Müller and Hartke (ref 1) used in the ReaxFF example, settings used for the ReaxFF parametrization, and visualization of some structures in the Müller and Hartke training set (PDF)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 9 publications.

    1. Loïc Dumortier, Céline Chizallet, Benoit Creton, Theodorus de Bruin, Toon Verstraelen. Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina. Journal of Chemical Theory and Computation 2024, 20 (9) , 3779-3797. https://doi.org/10.1021/acs.jctc.3c01009
    2. Mike Pols, Adri C. T. van Duin, Sofía Calero, Shuxia Tao. Mixing I and Br in Inorganic Perovskites: Atomistic Insights from Reactive Molecular Dynamics Simulations. The Journal of Physical Chemistry C 2024, 128 (9) , 4111-4118. https://doi.org/10.1021/acs.jpcc.4c00563
    3. Michael Freitas Gustavo, Matti Hellström, Toon Verstraelen. Sensitivity Analysis for ReaxFF Reparametrization Using the Hilbert–Schmidt Independence Criterion. Journal of Chemical Theory and Computation 2023, 19 (9) , 2557-2573. https://doi.org/10.1021/acs.jctc.2c01320
    4. Sander Raaijmakers, Mike Pols, José Manuel Vicent-Luna, Shuxia Tao. Refined GFN1-xTB Parameters for Engineering Phase-Stable CsPbX3 Perovskites. The Journal of Physical Chemistry C 2022, 126 (22) , 9587-9596. https://doi.org/10.1021/acs.jpcc.2c02412
    5. Leonid Komissarov, Toon Verstraelen. Improving the Silicon Interactions of GFN-xTB. Journal of Chemical Information and Modeling 2021, 61 (12) , 5931-5937. https://doi.org/10.1021/acs.jcim.1c01170
    6. Leonid Komissarov, Lukas Krep, Felix Schmalz, Wassja A. Kopp, Kai Leonhard, Toon Verstraelen. A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development. ChemPhysChem 2023, 122 https://doi.org/10.1002/cphc.202200786
    7. Michael Freitas Gustavo, Toon Verstraelen. GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations. Journal of Cheminformatics 2022, 14 (1) https://doi.org/10.1186/s13321-022-00581-z
    8. Sizhe Liu, Binquan Luan. Benchmarking various types of partial atomic charges for classical all-atom simulations of metal–organic frameworks. Nanoscale 2022, 14 (26) , 9466-9473. https://doi.org/10.1039/D2NR00354F
    9. Michael Freitas Gustavo, Toon Verstraelen. Reparameterization of Computational Chemistry Force Fields Using GloMPO (Globally Managed Parallel Optimization). 2021, 150-156. https://doi.org/10.1007/978-3-030-92121-7_13

    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2021, 61, 8, 3737–3743
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jcim.1c00333
    Published May 13, 2021
    Copyright © 2021 American Chemical Society

    Article Views

    1520

    Altmetric

    -

    Citations

    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.