VMD
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
| Tags | multimedia Graphics 3D Rendering Viewers Scientific/Engineering Bioinformatics Chemistry Medical Science Visualization |
|---|---|
| Operating Systems | Mac OS X Windows Windows Windows Windows POSIX Solaris |
| Implementation | C C++ Python Tcl |
Recent releases
- 29 Aug 2006 05:39
Changes: This release includes a new multiple sequence alignment bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids. The Mac OS X versions were updated for MacOS X 10.4 and now support stereoscopic display and OpenGL shading language. New collaboration plugins allow VMD users to chat, submit APBS and NAMD jobs to remote supercomputers and clusters, and exchange VMD views, all without the need to to install or run any additional software.
- 17 Apr 2006 14:40
Changes: This is the first version ported to Mac OS X on Intel x86 processors, Linux on Intel Itanium processors, and AIX 5.x on 32-bit and 64-bit POWER processors. Structure building, modeling, simulation setup, and analysis tasks are made easier with the introduction of the new plugins, which automate common modeling tasks. This release has core enhancements including support for selecting and displaying files containing multiple conformations, improved atomic mass and radius guessing, and improved handling of non-biological structures containing hundreds of thousands of atoms.
- 16 Mar 2006 03:17
Changes: This test version includes new ports to Mac OS X on Intel, Linux on Itanium, and 64-bit AIX5. New structure building plugins and many updated molecular file reader/writer plugins were included.
- 17 Mar 2005 22:47
Changes: This release feaures multiple structure alignment, sequence alignment, phylogenetic tree display, high-quality shading with OpenGL shading language support, new APBS electrostatic potential plugin, particle mesh ewald potential map plugin, new cartoon secondary structure representation, solvent accessible surface area calculations, coloring by volumetric datasets, and much more.
- 08 Dec 2003 11:37
Changes: OpenGL rendering performance improvements on all platforms. The Mac OS X version has been updated for 10.3. Eight new file reader plugins have been added, supporting new density and potential map file formats, and two new molecular dynamics restart file formats. Several trajectory reader plugins now support 64-bit file sizes. A new "draw multiple frames" feature can render trajectories of interesting parts of a simulated structure so their path over time can be seen all at once. Several user interface improvements, particularly with regard to working with volumetric data sets.
