A powerful and reliable molecular visualization program for displaying, animating and analyzing large biomolecular systems using 3-D graphics
What's new in VMD 1.9.3:
Jan 17, 2013. VMD 1.9.2 is a third party application that provides additional functionality to OS X system and enjoys a popularity among Mac users. However, instead of installing it by dragging its icon to the Application folder, uninstalling VMD 1.9.2 may need you to do more than a simple drag-and-drop to the Trash. Download VMD: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Visit the VMD website for complete information and documentation. Selecting an archive below will lead to a user registration and login page.
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 guides users 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, and to enable simulation workflows and protocols to be shared among users.
The Force Field Toolkit (ffTK) plugin provides a comprehensive toolset for the development 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.
Read the full changelog
(located in Programs→University of Illinois→VMD by default) Mac users: Run the.dmg file 1 To determine what type of processor is in your Mac, go to the Finder and choose About this Mac from the Apple Menu. VMD User Guide 3 VMD Input – PDB Files VMD.
VMD is the tool you need to use when you have to analyze proteins, lipid bilayer assemblies and nucleic acids.
The application allows you to view general molecules, and it even comes with complete support for the Protein Data Bank. It requires you to enter the ID or download the molecule, then it displays the protein structure in a snap.
VMD comes with multiple methods of coloring and rendering a molecule, by using CPK spheres, cartoon drawing, licorice bonds or cylinders.
The tool makes it easier to analyze and animate the trajectory of molecular dynamics. Furthermore, VMD acts as a GUI for an external MD program by animating a molecule simulation.
VMD comes with complete support for GPU accelerated computation and multicore processors. It doesn't have a limit for the number of atoms, residues, molecules and trajectory frames it can use, since these are limited only by the amount of memory you have installed on your Mac.
In addition, VMD provides the ability to export graphics to a file which can easily be processed by a large number of ray tracing applications.
VMD provides a multiple sequence alignment plugin but it also includes a bioinformatics environment created to organize structure data for nucleic acids and proteins.
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VMD 1.9.3
Namd Vmd
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runs on:
Mac OS X 10.4.7 or later (Intel only)
file size:
25.4 MB
filename:
vmd193macx86nocuda.dmg
main category:
Math/Scientific
developer:
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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.
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Recent releases
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.
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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.
Vmd 1.9.3
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.