MOLECULAR MODELING PROGRAM NAMD

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VMD is a visualization program developed by the Resource and designed for interactive display and analysis of biomolecular systems [13]. The program is capable of animation, manipulation and analysis of proteins, nucleic acids, lipid membranes and other biological molecules. It supports OpenGL and SGI GL graphics libraries with stereo displays. Moreover, VMD supports output formats for VRML (Virtual Reality Modeling Language) and many popular renderers (RayShade, POV-Ray and Raster3D). VMD can read many different file formats directly and through an interface with the program Babel [58]. The wide variety of methods for rendering and coloring molecules offered by VMD includes VdW, licorice, cartoon and surface models. Animation information can come from a trajectory file or by connecting to a running simulation program, such as NAMD [19, 59]. The VMD scripting language is based on TCL/TK. It may be used to query molecular information, perform analysis and display the res ults interactively, yielding a powerful base for implementing new methods in structure visualization and analysis. To further method development, the complete C++ source code is freely available to the biomedical community, along with documentation for using and modifying the program. Version 1.2 of VMD runs under most versions of Unix, including IRIX, Linux and Solaris, and will soon be ported to Windows NT. See the VMD home page for more information.*