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namd package  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc namd package
    Namd Package, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/namd+package/namd/bio_rxiv__64898__2026__02__27__708212-27-7-0
    Average 86 stars, based on 1 article reviews
    namd package - by Bioz Stars, 2026-09
    86/100 stars

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    Article Title: RadicalPy: A Tool for Spin Dynamics Simulations
    Article Snippet: Molecular dynamics simulations were performed using the NAMD package., The CHARMM36 force field was used for lipids and tryptophan , and additional parametrizations for FAD.

    Article Title: Revealing properties for enhanced quantum sensing in engineered proteins
    Article Snippet: Molecular dynamics simulations were performed using the NAMD package., The employed CHARMM36 force field included CMAP corrections for proteins , and additional parameterizations for FMN.

    Article Title: Assessing the role of zinc in the structure-stability-activity paradigm of bacteriophage T7 endolysin.
    Article Snippet: • Zn2+ as a cofactor significantly enhances the amidase activity of T7

    Article Title: Effects of Nicotine on the Thermodynamics and Phase Coexistence of Pulmonary Surfactant Model Membranes.
    Article Snippet: Molecular dynamics simulations of the nicotine-membrane interaction were performed using the NAMD package [43].

    Article Title: Mechanism of O 2 Activation for Conversion of Fatty Acids into Terminal Alkenes in a Membrane-bound Metalloenzyme UndB
    Article Snippet: Molecular dynamics (MD) simulations were performed using the GPU-accelerated version of the NAMD( ) package.

    Article Title: Effects of Nicotine on the Thermodynamics and Phase Coexistence of Pulmonary Surfactant Model Membranes
    Article Snippet: Molecular dynamics simulations of the nicotine-membrane interaction were performed using the NAMD package [ ].

    Construct:

    Article Title: RadicalPy: A Tool for Spin Dynamics Simulations.
    Article Snippet: Molecular Dynamics Simulations. .. The AOT (sodium bis(2-ethylhexyl) sulfosuccinate) water−isooctane system was constructed using the Micelle Maker online tool.43 Molecular dynamics simulations were performed using the NAMD package.44,45 The CHARMM36 force field was used for lipids and tryptophan46,47 and additional parametrizations for FAD.48−50 Periodic boundary conditions were adopted, and the Ewald summation method of the particle mesh was used to evaluate long-range Coulomb interactions. ..



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