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Molecular Dynamics Inc visual molecular dynamics software toolkit
Visual Molecular Dynamics Software Toolkit, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/visualization+toolkit+software/visual+molecular+dynamics+program/pm33625224-39-18-16
Average 90 stars, based on 1 article reviews
visual molecular dynamics software toolkit - by Bioz Stars, 2026-09
90/100 stars

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Article Title: Internal Cavity versus External Cavity: A Theoretical Study of Molecular Recognition of Biphenarene.
Article Snippet: Crystalline macrocyclic materials hold great promise for the efficient separation of compounds with similar structures and properties via selective molecular recognition.. Notably, the crystal packing of the macrocycles creates new intermolecular external cavities capable of accommodating guest molecules in a manner distinct from molecular recognition in solution, thereby exhibiting different adsorption properties.. This work focuses on the guest recognition mechanisms of MeBP3, a new type of macrocyclic arene, in a crystal environment.

Article Title: Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations.
Article Snippet: The MscL structures were rendered using the Visual Molecular Dynamics (VMD) program.39 We started with 12 replicas of the MscL mutant and equilibrated them at zero surface tension for 200 ns (the workflow of a single replica simulation is illustrated in Figure 2a).

Article Title: On the Engulfment of Antifreeze Proteins by Ice
Article Snippet: The snapshots were visualized using the Visual Molecular Dynamics (VMD) package (11).

Article Title: Stability of colloidal gas aphrons based on polymer-surfactant formulations and molecular dynamics insights
Article Snippet: To visualize and study the simulation results Visual Molecular Dynamics (VMD) tool was used .

Article Title: Cooperative Role of Mixed Solvent in the Evaporation-Induced Self-Assembly of Polypeptoid Nanocrystals
Article Snippet: The simulated structures were visualized using the Visual Molecular Dynamics (VMD) package.

Article Title: An Electrochromic Pure Poly( N -phenylglycine) with a High Optical Modulation Amplitude, a Wide Color Gamut, and Safe Raw Material Accessibility.
Article Snippet: Conductive polymer-based electrochromic materials (ECMs), distinguished by their wide color tunability and low cost, are limited particularly in terms of their optical modulation range and response time; meanwhile, their monomers pose significant risks to human health and the environment.. In this work, we report a nontoxic polyaniline (PANI)-based derivative, poly(N-phenylglycine) (PNPG).. By introducing carboxyl groups onto the nitrogen atoms of the polymer backbone, the conjugated and electronic structure of the polymer was modified, thus reducing the bandgap of PNPG and facilitating charge transportation.

Article Title: Oscillations in incident electric field enhances interfacial water evaporation.
Article Snippet: Visualization is performed in perspective display mode using the Visual Molecular Dynamics (VMD) package.44 (b) Water density profile along y-direction for both cases, i.e., with and without hydrogel.

Software:

Article Title: Internal Cavity versus External Cavity: A Theoretical Study of Molecular Recognition of Biphenarene.
Article Snippet: Crystalline macrocyclic materials hold great promise for the efficient separation of compounds with similar structures and properties via selective molecular recognition.. Notably, the crystal packing of the macrocycles creates new intermolecular external cavities capable of accommodating guest molecules in a manner distinct from molecular recognition in solution, thereby exhibiting different adsorption properties.. This work focuses on the guest recognition mechanisms of MeBP3, a new type of macrocyclic arene, in a crystal environment.

Article Title: Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations.
Article Snippet: The MscL structures were rendered using the Visual Molecular Dynamics (VMD) program.39 We started with 12 replicas of the MscL mutant and equilibrated them at zero surface tension for 200 ns (the workflow of a single replica simulation is illustrated in Figure 2a).

Article Title: On the Engulfment of Antifreeze Proteins by Ice
Article Snippet: The snapshots were visualized using the Visual Molecular Dynamics (VMD) package (11).

Article Title: Stability of colloidal gas aphrons based on polymer-surfactant formulations and molecular dynamics insights
Article Snippet: To visualize and study the simulation results Visual Molecular Dynamics (VMD) tool was used .

Article Title: Cooperative Role of Mixed Solvent in the Evaporation-Induced Self-Assembly of Polypeptoid Nanocrystals
Article Snippet: The simulated structures were visualized using the Visual Molecular Dynamics (VMD) package.

Article Title: An Electrochromic Pure Poly( N -phenylglycine) with a High Optical Modulation Amplitude, a Wide Color Gamut, and Safe Raw Material Accessibility.
Article Snippet: Conductive polymer-based electrochromic materials (ECMs), distinguished by their wide color tunability and low cost, are limited particularly in terms of their optical modulation range and response time; meanwhile, their monomers pose significant risks to human health and the environment.. In this work, we report a nontoxic polyaniline (PANI)-based derivative, poly(N-phenylglycine) (PNPG).. By introducing carboxyl groups onto the nitrogen atoms of the polymer backbone, the conjugated and electronic structure of the polymer was modified, thus reducing the bandgap of PNPG and facilitating charge transportation.

Article Title: Oscillations in incident electric field enhances interfacial water evaporation.
Article Snippet: Visualization is performed in perspective display mode using the Visual Molecular Dynamics (VMD) package.44 (b) Water density profile along y-direction for both cases, i.e., with and without hydrogel.



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