Vmd citation full#
Vmd citation software#
Vmd citation code#

The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. 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. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. 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. 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. 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. Special thanks go to Rick Kufrin of the National Center for Supercomputing Applications, the author of the MDCOMM software. 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.

Vmd citation code#

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.',

Vmd citation software#

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 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. 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 citation full#

Full session logging is supported, which produces a VMD command script for later playback. 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. 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.Ībstract = '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 is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids.