TY - JOUR
T1 - Using VMD
T2 - An introductory tutorial
AU - Hsin, Jen
AU - Arkhipov, Anton
AU - Yin, Ying
AU - Stone, John E.
AU - Schulten, Klaus
PY - 2008
Y1 - 2008
N2 - 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.
AB - 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.
KW - Animation
KW - Interactive visualization
KW - Molecular dynamics visualization
KW - Molecular modeling
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U2 - 10.1002/0471250953.bi0507s24
DO - 10.1002/0471250953.bi0507s24
M3 - Review article
C2 - 19085979
AN - SCOPUS:58849088534
SN - 1934-3396
SP - 5.7.1-5.7.48
JO - Current Protocols in Bioinformatics
JF - Current Protocols in Bioinformatics
IS - SUPPL. 24
ER -