VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

References in zbMATH (referenced in 89 articles )

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  1. Nikfar, Mohsen; Taati, Ehsan; Asghari, Mohsen: Dynamic pull-in instability of multilayer graphene NEMSs: non-classical continuum model and molecular dynamics simulations (2022)
  2. Zhao, Yan; Wang, Yanying; Ding, Yanhong; Han, Huiyun: Topological data analysis for the energy and stability of endohedral metallofullerenes (2022)
  3. Barclay, Paul L.; Zhang, Duan Z.: Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations (2021)
  4. Chen, Jiahui; Zhao, Rundong; Tong, Yiying; Wei, Guo-Wei: Evolutionary de Rham-Hodge method (2021)
  5. An, Dong; Lin, Lin: Quantum dynamics with the parallel transport gauge (2020)
  6. Teixeira, J. M.: taurenmd: A command-line interface for analysis of Molecular Dynamics simulations (2020) not zbMATH
  7. Hou, Yanzhen; Niemi, Antti J.; Peng, Xubiao; Ilieva, Nevena: Myoglobin ligand gate mechanism analysis by a novel 3D visualization technique (2019)
  8. Raos, Guido: Molecular geometry and molecular graphics: Natta’s polypropylene and beyond (2019)
  9. Robu, Andreea; Mironov, Vladimir; Neagu, Adrian: Using sacrificial cell spheroids for the bioprinting of perfusable 3D tissue and organ constructs: a computational study (2019)
  10. Salas, Gicela G. Saucedo; Hernandez, Alan E. Lopez; He, Jiadi; Karki, Chitra; Xie, Yixin; Sun, Shengjie; Xian, Yuejiao; Li, Lin: Using computational approaches to study dengue virus capsid assembly (2019)
  11. Younes Nejahi; Mohammad Soroush Barhaghi; Jason Mick; Brock Jackman; Kamel Rushaidat; Yuanzhe Li; Loren Schwiebert; Jeffrey Potoff: GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids (2019) not zbMATH
  12. Camiola, Vito Dario; Tozzini, Valentina: Collective mode mining from molecular dynamics simulations: a comparative approach (2018)
  13. Damle, Anil; Lin, Lin: Disentanglement via entanglement: a unified method for Wannier localization (2018)
  14. Fu, Yi; Zhao, Ji; Chen, Zhiguo; Chen, Xiaole: Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein (2018)
  15. Hudson, Robert B.; Sinha, Alok: Vibration of carbon nanotubes with defects: order reduction methods (2018)
  16. Jiang, Xi Zhuo; Feng, Muye; Luo, Kai H.; Ventikos, Yiannis: Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx (2018)
  17. Mezei, Mihaly: Revisiting chameleon sequences in the protein data bank (2018)
  18. Stritzler, Margarita; Berini, Carolina; Jozefkowicz, Cintia; Soto, Gabriela; Ayub, Nicolás: Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in \textitPseudomonasbackgrounds as a microevolutionary process (2018)
  19. Zhang, Yi Ran; Jiang, Xi Zhuo; Chen, Yi Ran; Luo, Kai Hong: Self-propelled jump regime in nanoscale droplet collisions: a molecular dynamics study (2018)
  20. Bu, Bing; Li, Dechang; Diao, Jiajie; Ji, Baohua: Mechanics of water pore formation in lipid membrane under electric field (2017)

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