Using VMD: An introductory tutorial

Jen Hsin, Anton Arkhipov, Ying Yin, John E. Stone, Klaus Schulten

Research output: Contribution to journalReview article

Abstract

VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assem-blies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins.

Original languageEnglish (US)
Pages (from-to)5.7.1-5.7.48
JournalCurrent Protocols in Bioinformatics
Issue numberSUPPL. 24
DOIs
StatePublished - Dec 1 2008

Fingerprint

Molecular Dynamics Simulation
Molecular dynamics
Drawing (graphics)
Lipid bilayers
Lipid Bilayers
Biological systems
Coloring
Nucleic Acids
Publications
Proteins
Visualization
Trajectories
Molecules
Computer simulation

Keywords

  • Animation
  • Interactive visualization
  • Molecular dynamics visualization
  • Molecular modeling

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry

Cite this

Hsin, J., Arkhipov, A., Yin, Y., Stone, J. E., & Schulten, K. (2008). Using VMD: An introductory tutorial. Current Protocols in Bioinformatics, (SUPPL. 24), 5.7.1-5.7.48. https://doi.org/10.1002/0471250953.bi0507s24

Using VMD : An introductory tutorial. / Hsin, Jen; Arkhipov, Anton; Yin, Ying; Stone, John E.; Schulten, Klaus.

In: Current Protocols in Bioinformatics, No. SUPPL. 24, 01.12.2008, p. 5.7.1-5.7.48.

Research output: Contribution to journalReview article

Hsin, J, Arkhipov, A, Yin, Y, Stone, JE & Schulten, K 2008, 'Using VMD: An introductory tutorial', Current Protocols in Bioinformatics, no. SUPPL. 24, pp. 5.7.1-5.7.48. https://doi.org/10.1002/0471250953.bi0507s24
Hsin J, Arkhipov A, Yin Y, Stone JE, Schulten K. Using VMD: An introductory tutorial. Current Protocols in Bioinformatics. 2008 Dec 1;(SUPPL. 24):5.7.1-5.7.48. https://doi.org/10.1002/0471250953.bi0507s24
Hsin, Jen ; Arkhipov, Anton ; Yin, Ying ; Stone, John E. ; Schulten, Klaus. / Using VMD : An introductory tutorial. In: Current Protocols in Bioinformatics. 2008 ; No. SUPPL. 24. pp. 5.7.1-5.7.48.
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