membrane
VMD 1.8.7 Beta 5 / 1.8.6
A molecular visualization program for displaying, animating and analyzing large biomolecular systems using 3-D graphics. more>> A molecular visualization program for displaying, animating and analyzing large biomolecular systems using 3-D graphics.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Mac OS X, UNIX, or Windows, is distributed free of charge, and includes source code.
VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes.
VMD is a general application for displaying molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities.
VMD includes built-in support for high-end quad-buffered stereoscopic rendering which can be used in projection theatres as well as desktop graphics workstations.
Sterescopic display aids significantly in the perception of three dimensional structures and has been a key feature in VMD since its first release. VMD also provides support for inexpensive game-oriented stereo glasses, and even anaglyphic (Red/Blue) stereo.
Main features:
- No limit on the number of molecules, atoms, residues or number of animation frames, except available memory.
- Many molecular and volumetric rendering and coloring methods.
- Extensive atom selection language with boolean and algebraic operators, regular expressions, distance based selections, and more.
- Extensive graphical and text interfaces to Tcl, Tk, and Python to provide powerful scripting and analysis capabilities.
- High-quality on-screen rendering using OpenGL programmable shading on advanced graphics accelerators.
- Stereoscopic display with shutter glasses, autostereoscopic flat panels, anaglyph stereo glasses, and side-by-side stereo viewing.
- 3-D interactive control through the use of joysticks, Spaceballs, haptic devices and other advanced input devices, with support for Virtual Reality Peripheral Network (VRPN).
- An extensible plugin-based file loading system with support for popular formats such as AMBER, CHARMM, Gromacs, NAMD, PDB, X-PLOR, and many others, as well as automatic conversion through Babel.
- Export displayed scene to extenal rendering formats including POV-Ray, Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well as STL or VRML2 files for 3-D printing.
- Integration of multiple sequence alignment and evolutionary analysis tools, in the form of the Multiseq plugin and its related toolset.
- Perform interactive molecular dynamics (IMD) simulations using NAMD, Protomol, or other programs as simulation back-ends.
- Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD. See the NAMD page for details: http://www.ks.uiuc.edu/Research/namd
- Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that collaborators can work together over the internet. See the BioCoRE page for details: http://www.ks.uiuc.edu/Research/biocore.
Version restrictions:
- You have to register in order to download.
Enhancements
- User documentation updates
- Minor improvements and corrections to the VMD Users Guide, added documentation for new commands and environment variables.
- New and updated tutorials available for advanced images and movie making, 3-D PDF export, Tachyon ambient occlusion lighting, electrostatic surface coloring, and density map based atom selections.
- User interface changes
- New "User" picking mode for use with user defined scripts and plugins
- General Improvements
- Support for 3-D capture with Acrobat 3-D, for creation of documents which embed 3-D molecular structures.
- VMD renderings can now use Tachyons advanced ambient occlusion lighting for tremendously improved 3-D renderings of molecular graphics. This advanced lighting mode can greatly enhance the shading of pores and channels, structures with cavities, and other cases which typically require the use of depth cueing for better depth perception.
- VMD now supports the nVidia "Gelato" GPU-accelerated production quality rendering package. VMD exports scenes in Gelatos native PYG file format, as well as the RenderMan RIB format.
- By default VMD will now use all of the available processors to accelerate parallelized portions of the code which currently include several structure analysis routines, Interactive MD, and ray tracing.
- Overall per-atom memory use has been significantly decreased. VMD now uses just over half as much memory per atom compared with previous versions, leaving more space available for additional trajectory frames or for more molecules to be loaded at once.
- VMD structure loading and analysis scalability have been significantly improved. VMD has been successfully tested loading and analyzing structures of up to 72,000,000 atoms.
- Automatic bond determination algorithm now runs up to 3 times faster on single processor systems, and uses multiple processors for improved performance on multicore processors and multiprocessor workstations.
- Drastically improved multi-thousand-file structure loading performance when display update is disabled. This benefits batch mode VMD analysis jobs involving analysis of thousands of structures, e.g. loading and searching large subsets of the PDB.
Wave Simulation 1.0
Wave Simulation is developed as a smart program which is simulative to a wave disturbance propagating on a two dimensional membrane. more>>
Wave Simulation 1.0 is developed as a smart program which is simulative to a wave disturbance propagating on a two dimensional membrane. The program uses a timer to step the simulation. At each step a two dimensional wave equation is solved by using a finite differencing scheme that is space centered and time forward. The initial conditions have been exaggerated for better visibility in the OpenGL output. See the commentary in the source code for further details. The idea here is to demonstrate simple numerical processing and scientific visualization in a Cocoa based application.
The program structure uses the Model/View/Controller paradigm. The classes for this structure are grouped under one heading and the various support classes are grouped under another heading. The View part of the program combines the user interface (UI) and the OpenGL rendering. The GLView class is a wrapper, i.e., sub-class, around the NSOpenGLView class that gives the class the ability to render, among other things, a mesh that is passed in from an outside source.
The view point and lighting that the GLView class uses in its rendering is also provided from outside. The visible part of the GLView in the UI is an outlet for the rendering. Also, the GLView object has been set up so that a mouse click in the visible rendering area toggle betwever, each update cycle is quick enough to justify a single threaded structure for the program.
An important characteristic of this program is that the OpenGL rendering is encapsulated in two parts of the program: the GLView class and the DrawingFunctions.h module. All of the other support classes make no reference to OpenGL. The Avian class is meant to capture the concept of an extended physical body that can have a location in 3D space as well as an orientation.
The FlyingCamera class is based on the Avian class and provides it with extras that are appropriate for handling views from various positions and orientations. The Mesh and MeshNode clases are also divorced from OpenGL. A GLView object 'knows' what to do with FlyingCamera and Mesh objects, but not vice versa. Also, the Controller object 'knows' how to relate user input, via the steppers, to FlyingCamera settings.
This program is also provides a good way to waste enormous quantities of time. The membrane uses a material that is meant to be a fair approximation of ruby. When the light is set to, say, colatitude equal to 35 degrees and longitude equal to 200 degrees the surface shows some nice highlights. Be warned: this program can induce a hypnotic state in the unwary user.
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