The Veterinary Medicines Directorate (VMD) protects animal health, public health and the environment. VMD is an executive agency, sponsored by the Department for Environment, Food & Rural Affairs.
VMD 1.9.3
The Theoretical and Computational Biophysics Group is pleased toannounce VMD version 1.9.3.VMD incorporates many new improvements for high qualityrendering and export of molecular scenes, new analysis features,support for new molecular data file formats, and manyperformance improvements.Many new and updated structure building and analysis tools havebeen added in this release, easing the process of preparing, running,and analyzing biomolecular simulations. This release alsocontains many performance and efficiency improvements that areparticiularly beneficial for modeling, visualizing, and analyzingvery large structures with over 100 million atoms.VMD makes extensive use of multi-core processors, vector instructionset extensions such as Intel SSE, AVX, and AVX-512, and IBM VSX, aswell as GPU acceleration to speed up computationally demanding analysisand visualization tasks including key structureand trajectory analysis features, interactive molecular dynamics,and high-quality ray tracing of molecular scenes.
- VMD 1.9.3 Development and Release History (large)
Major features included in VMD 1.9.3:
Connecting the user-friendly molecular graphics program VMD to the widely adopted MD program NAMD, the new QwikMD plugin guidesusers to prepare common molecular simulations in just a few minutes, allowing for quickly study of point mutations, partial deletions or even steering experiments. While making it easy for a new user to perform simulations, QwikMD also works as a learning tool with 'info buttons' that guide the user and provide the theoretical background underlying the procedures that are followed.Each 'info button' generates a window where the user can find fundamental information related to Molecular Dynamics simulations, such as the description of solvent models and protein structure, as well as short explanations of the options available in QwikMD graphical interface and the actions triggered by the buttons. For more information, the user is redirected to web-pages through links present in the bottom of the information window.QwikMD incorporates logging of procedures for reproducibility, andto enable simulation workflows and protocols to be shared among users.Documentation and tutorials are available on the plugin website, and the key attributes of the design andphilosophy behind QwikMD are reported here.The new QwikMD integrative modeling plugin assists with
preparation and analysis of molecular simulations,
as shown in this 'standard MD workflow' exampleThe Force Field Toolkit (ffTK) plugin provides a comprehensive toolset for thedevelopment of CHARMM-compatible (e.g., CGenFF) force field parameters,including charges, bonds, angles, and dihedrals. Two new major features have been added to the Force Field Toolkit for the VMD 1.9.3 release.The latest Force Field Toolkit plugin assists with
development of CHARMM-compatible parametersA new tool has been added to the BuildPar toolset that processes output from the CGenFF Program webserver to automatically construct all of the structural and parameter input required for entry into the ffTK parameterization workflow,bypassing a common stumbling block in structure preparation. The CGenFF Program web serverperforms an analysis of molecular structureand assigns parameters based on analogy to molecules contained with in thestandard CGenFF parameter set. ffTK can now leverage the output from thisresource to automatically prepare the PSF+PDB files required by ffTK, analyzepenalty scores associated with each returned parameter, visualize all instancesof a given parameter directly within the molecular structure, and write aparameter file that is initialized to the CGenFF values as a starting point forrefinement.A new analysis and plotting utility, named Torsion Explorer (accessable from the Scan Torsions tab), is designed specifically to aid in troubleshooting difficultdihedral parameter fits providing visual and numerical analysis of the relaxedQM torsion scans. The key function of this tool is to load each optimizedstructural conformation into VMD and to construct a color plot of the associatedpotential energy surface (PES) for side-by-side comparison. Numerical analysiscan also be performed to provide detailed information on how all dihedralschange throughout the scan, helping to identify highly coupled torsions thatoften complicate parameter fitting.In addition to the major tools described above, ffTK contains several new butsmaller features, such as the ability to output the MM relaxed conformationalscan used as the baseline in dihedral fitting, and bug fixes.Documentation and screencast tutorials are available on the plugin website.Left: New MDFF graphical interfaces for analysis and interactive simulation.VMD 1.9.3 contains several updates for the Molecular Dynamics Flexible Fitting (MDFF) Method.The MDFF setup plugin now supports the use of multiple density maps in a single MDFF simulation. The MDFF graphical user interface (GUI) in the Modeling section of the VMD Extensions menu has been updated to reflect the use of multiple maps in addition to many other usability improvements. The cispeptide, chirality, and the new TorsionPlot, and QwikMD plugins now connect to the MDFF GUI to simplify finding and fixing errors or setting up your structure for MDFF. Both the MDFF GUI and command line plugins now use CHARMM36 as the default parameter set.
Right: GPU-accelerated MDFF hybrid structure quality-of-fit
cross correlation analysis shown in the Timeline plugin.The collective variables module implemented in VMD (and shared with NAMD and LAMMPS)incorporates many new features and improvements, including: histogram calculation on ensembles of variables, with optional weights;probability distribution restraints analysis;newly contributed variable types 'dipoleAngle' (Alejandro Bernardin),'groupCoordNum' (Alan Grossfield);scripting command 'cvcflags' to optimize performance of complex colvars;and improved error handling in user input and scripting.VMD 1.9.3 contains many features for generatinghigh quality renderings of molecular graphics and for creationof movies of both static structures and molecular dynamics simulationtrajectories.Proto-cell with ambient occlusion lighting, shadows, depth-of-field
focal blur, and reflections, rendered with the newest GPU-accelerated
TachyonL-OptiX parallel ray tracing engine built-into VMDVMD includes an improvedbuilt-in GPU-accelerated version of the Tachyonray tracing engine, using NVIDIA CUDA and OptiX toachieve interactive ray tracing performance, even formolecular systems containing tens to hundreds of millions of particles.The improved GPU-accelerated 'TachyonL-OptiX' ray tracer supports the vast majority of Tachyon rendering features, with emphasison ambient occlusion lighting, shadows, depth-of-field,high quality transparent surface rendering, andparallel movie rendering forlarge complexes such as viruses, and cellular organelles.The new GPU ray tracing engine in VMD 1.9.3 supports the generation ofomnidirectional stereoscopic images and movies, suitable for use withYouTube VR movies, which are playable on a wide variety of VR headsetsbased on phones and computer-driven head mounted displays, includingGoogle Cardboard, GearVR, Oculus Rift, and others. A new VMD VR movie rendering minitutorial details the steps necessary for creating VR movie content forYouTube and VR headsets.VMD 1.9.3 also debuts a new built-in interactive CPU-based ray tracing engine based on Intel OSPRay, that allows systems based on Intel x86 CPUs and in particular the new Xeon Phi Knight's Landing processors to interactively display VMD scenes with ambient occlusion lighting, shadows, and depth-of-field, with support for parallel movie rendering.The new 'TachyonL-OSPRay' renderer in VMD 1.9.3 achieves higher performancethan the standard Tachyon renderer, and supports many of the most widely usedVMD materials and shading features. The new OSPRay-based ray tracing enginein VMD is outlined in this recent article.The updatedViewChangeRenderplugin provides an easy-to-use graphical interface for managing multipleVMD camera viewpoints and making movies that fly the camera betweenmultiple viewpoints.The latest version of ViewChangeRender also supportsimproved parallel movie rendering on clusters and supercomputers.VMD molecular scenes with depth-of-field focal blur,
ambient occlusion lighting, and shadows, rendered with the
interactive ray tracing engines built-into VMDThe speed of the new interactive ray tracing engines in VMD 1.9.3 allow users to interactively visualize moderate size molecular complexescontaining a few million atoms with shadows, ambient occlusion. Even the depth-of-field focal blur effect can be rendered in real-time onrecent hardware.The interactive ray tracing engines use progressive refinementto allow users to manipulate the view using the mouse, andonce the mouse is released, the image is refined with monte carlo sampling of lighting, focal blur, and so on.The interactive ray tracing engines allow multiple views to be savedat any time, as well as the default behavior of saving the final imageshown when the user exits the viewer. Future versions of VMD willmore closely integrate interactive ray tracing, enabling interactiveray tracing in the main VMD window, as an alternative to the traditionalOpenGL-based visualization engine in VMD.As reported in several publications,VMD uses GPUs to accelerate many of the most computationally demandingvisualization and analysis features of interest to biomedical researchers.VMD 1.9.3 advances these capabilities further, adding support for thelatest generation of NVIDIA 'Pascal' GPUs. The new version includes animproved GPU-accelerated implementation of the QuickSurfmolecular surface representation which can now handle rendering of large biomolecular complexes andcellular organelles containing several hundred million particles,with significant improvements for the display of coarse-grained modelsof such as proto-cell membranes.The QuickSurf representation enables smooth interactive animation ofmoderate sized biomolecular complexes consisting of a few hundred thousandto one million atoms, and interactive display of molecular surfaces formulti-million atom complexes such as virus capsids.The range of acceleration provided by GPUs depends on thecapabilities of the specific GPU device(s) installed, and the detailsof the calculation. Typical (approximate) acceleration factors for the algorithms in VMDcomparing a single high-end GPU vs. a single quad-core CPU are: molecular surface display 2.5x to 11x, electrostatics 5x to 11x, implicit ligand sampling 4x to 7.5x, calculation of radial distribution functions 7.5x to 22x, molecular orbital calculation 10x to 30x.Details on making best use of the GPU acceleration capabilitiesin VMD are provided here.Fast 'QuickSurf' multi-resolution molecular surface
calculation and display with CUDA GPU accelerationVMD 1.9.3 adds support for the new Cray XC50 supercomputer with compute nodes that combine the latest Intel Xeon CPUs and NVIDIA P100 GPU accelerators utilizing die-stacked memory.The new version of VMD also adds support for workstations, clusters, and supercomputers based on the new IBM POWER8 (OpenPOWER) and Intel Xeon Phi (Knight's Landing) CPUs to be used in the DOE/ORNL Crest (OpenPOWER/NVLink/Tesla P100), NSF/TACC Stampede-2 (Dell/Intel KNL),and DOE/ALCF Theta (Cray/Intel KNL)systems.New hand-vectorized CPU kernels for commonly usedVMD analysis and visualization algorithms increase performance significantly beyond standard C++ on both platforms,making advantageous use of the native VSX and AVX-512 vector instruction sets on each processor, respectively.VMD 1.9.3 supports the new CPUs and GPUs used in the latest
clusters and supercomputers at NSF/TACC Stampede-2 (left),
DOE/ALCF Theta (right), DOE/ORNL Crest, NSF/PSC Bridges-2,
and the new CSCS/ETHZ Piz Daint Cray XC50.The new OpenPOWER version of VMD supports CUDA GPU acceleration forkey analysis kernels, and benefits from the large memory capacity andmemory bandwidth available on these systems,as reported here.VMD takes advantage of the high performance NVLink CPU-GPU interconnecton the new IBM 'Minsky' platform containing POWER8 CPUs paired with NVIDIA Tesla P100 GPUs, shown with some early performance results hereThe new Intel Xeon Phi AVX-512 version of VMD has been developed to exploit the wide 16-element SIMD units for key analysis and visualization tasks, incorporating new hand-written AVX-512 analysis kernels and support forthe Intel OSPRay ray tracing engine optimized for the new Xeon Phi processors, as shown with someearly performance results here.VMD 1.9.3 incorporates initial support for a variety of ARM processors paired with GPU accelerators (on-chip and/or add-in-board). Due to lackof standardization among ARM operating system distributions, ARM platformscurrently require compilation from the VMD source code. Results of earlyperformance tests on GPU-accelerated ARM platforms and associatedoptimizations have been reported here.One of the features of VMD 1.9.3 is support for off-screenrasterization on clouds, clusters, and supercomputers, through the useof the latest Embedded GL (EGL) graphics APIs for managing OpenGLcontexts and rendering surfaces. With EGL, it is no longer necessary for a compute node to have a complete windowing system installation tobe able to perform routine post-hoc molecular visualization tasks inplace on compute nodes where the data are generated and stored, therebyeliminating the need for time consuming data staging and file transfer activities. The use of EGL eliminates the need for specialcompilations of VMD for GPU-accelerated or software-based rasterization,eliminating many of the technical hurdles and administrative tasks thatwould have previously been required for deployment of a full OpenGL-enabledVMD installation on large parallel computers.The new EGL-based graphics feature in VMD supports all of the standard VMD OpenGL features including pixel-rate lighting,multisample antialiasing, high quality transparency, text rendering,and all of the standard VMD materials and shading features, as reported here.VMD 1.9.3 adds support for off-screen rasterization on clouds, clusters,
and supercomputers without the need for installing or running
windowing system software using the Embedded GL (EGL) graphics API.
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