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gaussian 16 software package 62 molecular dynamics simulations  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc gaussian 16 software package 62 molecular dynamics simulations
    Gaussian 16 Software Package 62 Molecular Dynamics Simulations, 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/dynamic+system+simulation+software/gaussian/pm40878658-107-8-12
    Average 86 stars, based on 1 article reviews
    gaussian 16 software package 62 molecular dynamics simulations - by Bioz Stars, 2026-09
    86/100 stars

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    other:

    Article Title: DualPG-DTA: A Large Language Model-Powered Graph Neural Network Framework for Enhanced Drug-Target Affinity Prediction and Discovery of Novel CDK9 Inhibitors Exhibiting in Vivo Anti-Leukemia Activity.
    Article Snippet: Molecular Dynamics Simulation: Molecular charges were calculated using Gaussian HF/6-31G* with the RESP fitting method.

    Software:

    Article Title: A detailed DFT inspection on the trapping of aspirin from drinking water using B 12 N 12 nanocage.
    Article Snippet: .. NCI (Non-Covalent interactions) 56 and NBO (natural bond orbital) 57 analyses were performed to characterize non-covalent interactions and charge transfer between the monomers utilizing the Multiwfn 3.6 58 (http://sobereva.com/multiwfn/), VMD (Visual Molecular Dynamics) 1.9.4 59, and Gaussian 16 software (https://seagrid.org/). ..

    Article Title: Cosolvent Electrolyte Design for Li-S Batteries: Suppressing the Shuttle Effect via Phase Separation.
    Article Snippet: Lithium–sulfur batteries are promising candidates for next-generation energy storage due to their high energy density and low cost.. However, their commercialization is hindered by poor cycling performance caused by the polysulfide shuttle effect.. While strategies such as physical barriers or chemical adsorption have been proposed, they inevitably introduce inactive components, reducing energy density.

    Article Title: Design of spherical particles in water for high-melting drugs through eutectic-assisted droplet-confined crystallization
    Article Snippet: This work presents a eutectic-assisted spherical crystallization for high-melting drugs using an organic solventfree method.. The approach involves creating a eutectic mixture of a high-melting drug, indomethacin, and the additive 2,6-dimethoxyphenol which is a low-melting food flavoring.. Water is subsequently added to selectively dissolve the additive, resulting in the formation of drug droplets that serve as the confinement for spherical crystallization.

    Functional Assay:

    Article Title: Cosolvent Electrolyte Design for Li-S Batteries: Suppressing the Shuttle Effect via Phase Separation.
    Article Snippet: Lithium–sulfur batteries are promising candidates for next-generation energy storage due to their high energy density and low cost.. However, their commercialization is hindered by poor cycling performance caused by the polysulfide shuttle effect.. While strategies such as physical barriers or chemical adsorption have been proposed, they inevitably introduce inactive components, reducing energy density.

    Article Title: Advancing the CL&Pol Polarizable Force Field for Accurate Modeling of Mg 2+ , Ca 2+ , and Zn 2+ Electrolytes.
    Article Snippet: Divalent cations such as Mg2+, Ca2+, or Zn2+ are promising candidates for powerful and affordable post-Li batteries due to their high natural abundance and an expected two-electron transfer per charge carrier.. But an accurate representation of divalent cations in electrolytes by molecular dynamics simulations remains challenging due to the effects of their high charge density.. For ionic systems such as the ones studied here, a molecular interaction model with explicit polarization terms, using Drude induced dipoles, largely improves the representation of equilibrium and transport properties when compared to fixed-charge models.

    Article Title: Design of spherical particles in water for high-melting drugs through eutectic-assisted droplet-confined crystallization
    Article Snippet: This work presents a eutectic-assisted spherical crystallization for high-melting drugs using an organic solventfree method.. The approach involves creating a eutectic mixture of a high-melting drug, indomethacin, and the additive 2,6-dimethoxyphenol which is a low-melting food flavoring.. Water is subsequently added to selectively dissolve the additive, resulting in the formation of drug droplets that serve as the confinement for spherical crystallization.

    Article Title: Short-Range Machine-Learning Potentials for Aqueous Electrolyte Solutions.
    Article Snippet: .. G. Lippert, J. Hutter, and M. Parrinello, “The Gaussian and Augmented-Plane-Wave Density Functional Method for Ab Initio Molecular Dynamics Simulations,” Theoretical Chemistry Accounts 103 (1999): 124. ..



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    Molecular Dynamics Inc molecular dynamics simulation software
    Results of <t>molecular</t> <t>dynamics</t> <t>simulation.</t> (A) RMSD variation curve; (B) fluctuation of amino acid residues; (C) Rg curve; (D) SASA fluctuation curve; (E) Number of H bonds. RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, gyration; SASA, solvent-accessible surface area; H-bonds, hydrogen bonds.
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    Molecular Dynamics Inc gaussian 16 software package 62 molecular dynamics simulations
    Results of <t>molecular</t> <t>dynamics</t> <t>simulation.</t> (A) RMSD variation curve; (B) fluctuation of amino acid residues; (C) Rg curve; (D) SASA fluctuation curve; (E) Number of H bonds. RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, gyration; SASA, solvent-accessible surface area; H-bonds, hydrogen bonds.
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    Results of molecular dynamics simulation. (A) RMSD variation curve; (B) fluctuation of amino acid residues; (C) Rg curve; (D) SASA fluctuation curve; (E) Number of H bonds. RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, gyration; SASA, solvent-accessible surface area; H-bonds, hydrogen bonds.

    Journal: Molecular Medicine Reports

    Article Title: Dihydroalterperylenol from endophytic fungus Alternaria semiverrucosa and its antitumour activity uncovered by transcriptome analysis, molecular docking and molecular dynamics simulations

    doi: 10.3892/mmr.2025.13740

    Figure Lengend Snippet: Results of molecular dynamics simulation. (A) RMSD variation curve; (B) fluctuation of amino acid residues; (C) Rg curve; (D) SASA fluctuation curve; (E) Number of H bonds. RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, gyration; SASA, solvent-accessible surface area; H-bonds, hydrogen bonds.

    Article Snippet: LH and ZH were responsible for the application and implementation of the Molecular dynamics simulation software.

    Techniques: Solvent

    Molecular dynamics simulation energy analysis. (A) Energy contribution of each amino acid residue in the protein-ligand complex (BMP2-1rew); (B) Total binding energy of the protein-ligand complex (BMP2-1rew); (C) Energy contribution of each amino acid residue in the protein-ligand complex (ID1-6mgn); (D) Total binding energy of the protein-ligand complex (ID1-6mgn); (E) Energy contribution of each amino acid residue in the protein-ligand complex (TGIF2-2dmn); (F) Total binding energy of the protein-ligand complex (TGIF2-2dmn).

    Journal: Molecular Medicine Reports

    Article Title: Dihydroalterperylenol from endophytic fungus Alternaria semiverrucosa and its antitumour activity uncovered by transcriptome analysis, molecular docking and molecular dynamics simulations

    doi: 10.3892/mmr.2025.13740

    Figure Lengend Snippet: Molecular dynamics simulation energy analysis. (A) Energy contribution of each amino acid residue in the protein-ligand complex (BMP2-1rew); (B) Total binding energy of the protein-ligand complex (BMP2-1rew); (C) Energy contribution of each amino acid residue in the protein-ligand complex (ID1-6mgn); (D) Total binding energy of the protein-ligand complex (ID1-6mgn); (E) Energy contribution of each amino acid residue in the protein-ligand complex (TGIF2-2dmn); (F) Total binding energy of the protein-ligand complex (TGIF2-2dmn).

    Article Snippet: LH and ZH were responsible for the application and implementation of the Molecular dynamics simulation software.

    Techniques: Residue, Binding Assay

    Free energy landscape of molecular dynamics simulation. (A) BMP2-1rew; (B) ID1-6mgn and (C) TGIF2-2dmn. RMSD, root mean square deviation

    Journal: Molecular Medicine Reports

    Article Title: Dihydroalterperylenol from endophytic fungus Alternaria semiverrucosa and its antitumour activity uncovered by transcriptome analysis, molecular docking and molecular dynamics simulations

    doi: 10.3892/mmr.2025.13740

    Figure Lengend Snippet: Free energy landscape of molecular dynamics simulation. (A) BMP2-1rew; (B) ID1-6mgn and (C) TGIF2-2dmn. RMSD, root mean square deviation

    Article Snippet: LH and ZH were responsible for the application and implementation of the Molecular dynamics simulation software.

    Techniques: