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 POSIX Solaris|
|Implementation||C C++ Python Tcl|
Release Notes: A new "QuickSurf" molecular surface representation allows molecular dynamics trajectories to be animated for selections of 10,000 to well over 100,000 atoms depending on the speed of the host machine. The new Force Field Toolkit (FFTK) plugin is a set of tools that aids users in the development of CHARMM-compatible force field parameters. A new graphical interface to allow results from ProPKA runs to be interactively displayed in VMD. A new Android phone/tablet remote control is included in this release. Many other new and updated plugins are described on the VMD home page.
Release Notes: Support for several new stereoscopic display modes. Improved export of molecular scenes to Wavefront OBJ format, for animation and rendering tools such as Autodesk Maya. Export of molecular scenes to X3D and X3DOM for interactive display of molecules in WebGL capable browsers. Many improvements to ray tracing and movie making features. Multi-GPU CUDA acceleration of quantum chemistry molecular orbital display. Initial support for OpenCL GPU acceleration and MPI parallel analysis of molecular dynamics trajectories. Many new and improved structure building and analysis plugins.
Release Notes: Support for NVIDIA CUDA was added on Mac OS X, both 32-bit and 64-bit Linux, and Windows. VMD now supports CUDA-based GPU acceleration for electrostatics calculations, for implicit ligand sampling, and for acceleration of molecular orbital display. The Windows version now supports multi-core processors. New "PaperChain" and "Twister" graphical representations were added for display of carbohydrate structures in VMD. The "Polyhedra" representation was added for display of silicon nanodevice structures. The "Orbital" representation displays and animates molecular orbitals associated with quantum chemistry simulations.
Release Notes: 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.
Release Notes: 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.