TY - JOUR
T1 - VMD
T2 - Visual molecular dynamics
AU - Humphrey, William
AU - Dalke, Andrew
AU - Schulten, Klaus
N1 - Funding Information:
We thank all contributors to VMD, including Ken Hamner and Jim Phillips at the University of Illinois, and Jon Leech at the University of North Carolina, as well as the main authors of NAMD, Mark Nelson, Attila Gursoy, and Robert Brunner. Special thanks go to Rick Kufrin of the National Center for Supercomputing Applications, the author of the MDCOMM software. We also thank the members of the Theoretical Biophysics group at the University of Illinois, who have been tremendously helpful in making suggestions and testing the program. This work is supported by grants from the National Institutes of Health (PHS 5 P41 RR05969-04), the National Science Foundation (BIR-9318159), and the Roy J. Carver Charitable Trust.
PY - 1996
Y1 - 1996
N2 - VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more 'representations,' in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
AB - VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more 'representations,' in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
KW - Interactive visualization
KW - Molecular dynamics visualization
KW - Molecular modeling
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U2 - 10.1016/0263-7855(96)00018-5
DO - 10.1016/0263-7855(96)00018-5
M3 - Article
C2 - 8744570
AN - SCOPUS:0029878720
VL - 14
SP - 33
EP - 38
JO - Journal of Molecular Graphics and Modelling
JF - Journal of Molecular Graphics and Modelling
SN - 1093-3263
IS - 1
ER -