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openmm simulation engine (Molecular Dynamics Inc)

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Molecular Dynamics Inc openmm simulation engine
Openmm Simulation Engine, 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/simulation+engine/dynamics+engine+molecular+openmm/pmc13065851-254-7-0
Average 86 stars, based on 1 article reviews

openmm simulation engine - by Bioz Stars, 2026-11

86/100 stars

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Article Title: Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics.
Article Snippet: A.; Amaro, R. E. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.

Article Title: Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.
Article Snippet: A.; Amaro, R. E. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.

Article Title: Stoichiometric binding of Cyclophilin-A to the HIV-1 capsid modulates its mechanoelastic properties
Article Snippet: All simulations were performed using the NAMD molecular dynamics engine (version 3 alpha 13)[ ], employing the GPU-resident mode for heating, equilibration and AFM nanoindentation simulations, and CPU-only mode for energy minimization [ ].

Article Title: The Allosteric Communication Network in the Activation of Antithrombin by Heparin
Article Snippet: Molecular dynamics simulations were performed using the OpenMM engine on the energy-minimized structures (AT_minimized.pdb).

Article Title: Unveiling the Transgalactosylation Switch of a GH42 β‑Galactosidase from the Infant Isolate Bifidobacterium breve DSM20213
Article Snippet: The model was subsequently simulated using the openMM molecular dynamics software (version 8.2).

Article Title: Carvacrol from Moringa oleifera as a potential antidiabetic agent using integrated in-silico approach inhibiting TCF7L2
Article Snippet: Molecular dynamics (MD) simulations of the TCF7L2–carvacrol complex were performed using the OpenMM simulation engine with the AMBER ff19SB force field for the protein and GAFF/GAFF2 parameters for the ligand.

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Article Title: AI fragmentation-based optimization of Sorafenib derivatives targeting VEGFR2 for angiogenesis-related pathologies: a structure-based in-silico study.
Article Snippet: .. Molecular dynamics simulations were performed using the OpenMM simulation engine, which was selected for its high computational efficiency, flexibility, and reproducibility in biomolecular simulations, as well as its extensive validation in protein–ligand interaction studies. ..

Article Title: AI fragmentation-based optimization of Sorafenib derivatives targeting VEGFR2 for angiogenesis-related pathologies: a structure-based in-silico study
Article Snippet: .. Molecular dynamics simulations were performed using the OpenMM simulation engine, which was selected for its high computational efficiency, flexibility, and reproducibility in biomolecular simulations, as well as its extensive validation in protein–ligand interaction studies. ..

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