VMD Key Features of Recent Release
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1 VMD Key Features of Recent Release John Stone Research/vmd/
2 Quick Summary of Features Broader platform support Updated user interfaces Accelerated analysis, rendering, display: multi-core CPUs, GPUs (CUDA) New graphical representations Many new rendering features New analysis features, atom selection commands New and updated VMD plugins
3 Updated User Interfaces New color scheme New rendering controls 6DOF input w/ Spacenavigator
4 Supported Platforms Standard Builds: MacOS X 10.4.x (PowerPC/x86) MacOS X 10.5.x (x86 + CUDA) Linux (32-bit/64-bit x86 + CUDA) Solaris 10 (64-bit Sparc/x86) Windows XP/Vista/7 (32-bit x86 + CUDA) Text-mode Analysis Builds: AIX 6.x (64-bit Power) Linux (64-bit PowerPC) Many more platforms via builds from source
5 Multi-core Acceleration Multi-core CPUs now supported on all VMD platforms, they speed up a broad range of features: within distance-based atom selections molecular orbital representation electrostatic map calculations calculation of radial distribution functions implicit ligand sampling distance-based bond search interactive molecular dynamics CAVE/FreeVR virtual reality displays
6 GPU Acceleration (CUDA) Electrostatic field calculation, ion placement: factor of 20x to 44x faster Molecular orbital calculation and display: factor of 120x faster Imaging of gas migration pathways in proteins with implicit ligand sampling: factor of 20x to 30x faster
7 Photobiology of Vision and Photosynthesis Investigations of the chromatophore, a photosynthetic organelle Light Partial model: ~10M atoms Electrostatics needed to build full structural model, place ions, study macroscopic properties Electrostatic field of chromatophore model from multilevel summation method: computed with 3 GPUs (G80) in ~90 seconds, 46x faster than single CPU core Full chromatophore model will permit structural, chemical and kinetic investigations at a structural systems biology level
8 Visualization of Quantum Chemistry Simulations New Orbital graphical representation Plugin interfaces extended for QM information New plugin for GAMESS Plugins for Gaussian and other QM packages indevelopment Fast: uses SSE, multi-core CPUs, and GPUs for speed C 60
9 Visualization of Carbohydrates, Multi-branched Structures New PaperChain and Twister graphical representations Draw ring structures, colored by pucker Ribbon-like representations for multibranched structures C 60
10 VMD Outline Material Property Accentuates the edges of surfaces Render CG systems with uniform particle types Can be used to emulate David Goodsell s renderings Good for grayscale renderings Supported in GLSL mode, Tachyon renderings
11 VMD Outline Material Property
12 VMD Outline Material Property
13 VMD/Tachyon Rendering Advancements: Ambient Occlusion Lighting Diffuse omnidirectional lighting Creates soft shadows Enhances shape perception, visibility of pockets and cavities Built-in AO GUI controls New VMD/Tachyon renders AO over 10 times faster than before
14 Ambient Occlusion Rendering Examples
15 Ambient Occlusion Rendering Examples
16 Ambient Occlusion Rendering Examples
17 VMD/Tachyon Volumetric Coloring Color by potential, density, other volumetric data Applies to any representation Most commonly used with surfaces, field lines, etc. Can now be combined with AO rendering via Tachyon
18 Volumetric Coloring Example
19 Internal Tachyon Renderer TachyonInternal now available on all platforms Directly renders VMD scene to output image file without making intermediate.dat files Greatly reduced I/O time and disk space usage enables much faster rendering of high quality movies
20 New/Updated Analysis Features New atom selection keywords: withinbonds select atoms connected within N or fewer bonds from candidate selection ringsize find rings structures containing N atoms maxringsize find rings containing up to N atoms New atom selection value fields (or queries): user2, user3, user4 per-atom, per-timestep data fields for use by user scripts pucker return Cremer-Pople pucker for a selected ring structure (size 5 or 6) vx, vy, vz per-atom, per-timestep velocities
21 New/Updated Analysis Features Meausre commands: measure surface find atoms on the surface of a selection measure inertia compute COM, axes of inertia, moments of inertia, etc measure symmetry finds molecular symmetry for an atom selection Many others, see VMD User s Guide for details on new and updated measure commands, atom selection keywords, etc.
22 New and Updated Plugins: Research/vmd/plugins/ Structure building Analysis Visualization Further discussion of new plugins in Wednesday and Friday sessions
23 Future VMD Development
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