We are continually adding new features to VMD (and expanding the spotlight to highlight more of the existing features of VMD) so come back and visit often.


VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow large-size and long-timescale simulation trajectories to be loaded into physical memory and accommodate large volumetric datasets. The 64 million atom HIV capsid simulation described in the May 30, 2013 issue of Nature is a first-class example of what can be done with VMD on an appropriately equipped graphics workstation. The HIV-1 model was prepared for simulation using the structure building tools and scripting features of VMD were later used for trajectory analysis. The all-atom structure of the HIV-1 capsid shown on the Nature cover was rendered within VMD using the internal Tachyon ray tracing engine, and was then composited with an artistic representation of the viral envelope and the Nature cover text.

Human immunodeficiency virus type 1 (HIV-1) is the major cause of AIDS, for which treatments need to be developed continuously as the virus becomes quickly resistant to new drugs. When the virus infects a human cell it releases into the cell its capsid, a closed, stable container protecting the viral genetic material. However, interaction with the cell triggers at some point an instability of the capsid, leading to a well timed release of the genetic material that merges then with the cell's genes and begins to control the cell. The dual role of the capsid, to be functionally both stable and unstable, makes it in principle an ideal target for antiviral drugs and, in fact, treatments of other viral infections successfully target the respective capsids. The size of the HIV-1 capsid (about 1,300 proteins), and its irregular shape had prevented so far the resolution of a full capsid atomic-level structure. However, in a tour de force effort, groups of experimental and computational scientists have now resolved the capsid's chemical structure (deposited to the protein data bank under the accession codes 3J3Q and 3J3Y). As reported recently (see also journal cover), the researchers combined NMR structure analysis, electron microscopy and data-guided molecular dynamics simulations utilizing VMD to prepare and analyze simulations performed using NAMD on one of the most powerful computers worldwide, Blue Waters, to obtain and characterize the HIV-1 capsid. The discovery can guide now the design of novel drugs for enhanced antiviral therapy. More information is available on our virus website, in video, and in a press release.
HIV-1 Capsid

See also movie: 15.5MB
made with VMD


VMD is frequently used to make figures and illustrations that grace the cover pages of textbooks and journals. The cover image on the August 2008 issue of Science by Klein and Shinoda demonstrates the use of VMD for visualization of large coarse-grain molecular dynamics trajectories. The image illustrates a simulation of a vesicle interacting with a lipid bilayer, with over 1 million coarse-grained interaction sites, equivalent to over 10 million atoms. Read more about their work here.

Since its inception, VMD was designed to take advantage of graphics processing units (GPUs) for interactive renderings of large biomolecular complexes. Recently, GPUs have become programmable and their massive parallel processing capabilities can now be utilized for non-graphical computations. VMD makes uses of this type GPU-based parallel computation to greatly accelerate calculation of electrostatic potential fields, used for visualization and analysis, and for modeling operations such as ion placement. Ongoing VMD development efforts will expand the use of GPU acceleration even further, for acceleration of volumetric processing, structure and trajectory analysis, and compute-limited operations performed within VMD and it's plugins. More information on GPU acceleration of molecular modeling applications is provided here.
Placement of ions in the ribosome

Globins are oxygen-storing proteins, vital to life. In our blood, hemoglobins carry oxygen from our lungs to every cell in our body. In our muscles, myoglobins keep reserves of oxygen to make sure it is available when needed. In some plants, leghemoglobins capture oxygen molecules that would otherwise be harmful to the production of ammonium necessary for the plant's survival. All these globins possess an iron-containig "heme", that grabs on to oxygen for a short time, and share the same protein architecture, despite large variations in their sequences. Since the heme group is buried inside a globin, scientists wondered how oxygen makes its way inside the protein to reach it. Exploring the motion and energetics of globins using the program NAMD researchers learned to gather data that permitted them to visualize, utilizing the VMD software, all the pathways taken by oxygen migrating inside whale myoglobin (see the Aug 2006 highlight and related publication). However, when the researchers turned their attention to the rest of the globin family to compute their oxygen pathways, they found, on their computational spelunking trip, something surprising. Given the conserved architecture of all globins, they expected to see similar oxygen pathways throughout the globin family, but they saw the opposite! Aside from a conserved pocket right at the heme binding site, the distribution of oxygen pathways showed very little similarity from one globin to the next. This result is described in a recent report, which shows that oxygen-pathways are not conserved by evolution, and that their location is not determined by a protein's overall architecture, but rather by its local amino acids. The researchers also learned which amino acids are found more often than others lining oxygen pathways, recognizing that bulky side groups are not hindering, but favoring oxygen passage. More information can be found here.
O2 pathways in trematode hemoglobin

Modern computers include a massively parallel graphics processing unit (GPU) designed to perform geometry and lighting calculations at blistering speeds. State of the art GPUs can perform 0.5 teraFLOPS with their hundred cores. The tremendous computational power of GPUs was untapped by scientific computations because it could only be accessed with difficulty until now. As reported in the Journal of Computational Chemistry, recent advances allowing GPUs to be used for general purpose computing have boosted the performance of a number of molecular modeling applications, including NAMD simulations and VMD electrostatic potential calculations. The accelerated versions of these applications run five to one hundred times faster than on the best CPU-based hardware, allowing a single desktop computer equipped with a GPU to provide processing power equivalent to an entire, large computing cluster. More information on GPU acceleration of molecular modeling applications is provided here.
Placement of ions in the ribosome

The cells of higher organisms store their genetic material, the genome, in the so-called nucleus where they organize transcription of DNA into messenger-RNA, the blueprint for proteins. The messenger-RNA leaves the cell to be decoded by ribosomes that synthesize the respective proteins. Transcription factors, also proteins, control in the nucleus which parts of the cells' genomes are transcribed. Naturally, the access to the nucleus as well as exit from it must be restricted to transcription factors and related biomolecules. This is achieved by the nuclear pores, wide channels lined with brushes of polymers. The polymers are disordered proteins and prevent passage for most cellular proteins, except for so-called transport factors which bus transcription factors, messenger RNA, and certain larger biomolecule into and out of the nucleus. How transport factors are permitted to pass the nuclear pores, despite many studies, has been largely unknown. Molecular dynamics simulations, based on relevant crystallographic structures, using NAMD provided a comprehensive picture on the passage mechanism as reported recently. The simulations, analyzed with VMD, revealed that transport factors are dotted rather regularly on their surface with spots that bind to the brushes of nuclear pore proteins. While any protein may accidentally exhibit such a binding spot or two, only transport factors offer a regular pattern of such spots on their surface that apparently is their passport permitting them movement into and out of the nucleus, i.e., helping them to glide through the pores' protein brushes. More on simulations of transport factors can be found here.
Cse1p

image size:
movie: 4.6MB
made with VMD


Because oxygen gas is very reactive, it is frequently employed by the cell as a reagent by proteins called enzymes, which build the organic compounds that the cell needs. One such enzyme belongs to the copper amine oxidase family. These proteins transform amine-containing compounds into molecules needed by the cell, by reacting the compounds with oxygen. Researchers have long been interested in finding out how the various reagents reach the buried copper active site before the final oxidation reaction can occur. While copper amine oxidases exhibit an obvious channel for capturing the amine compounds to be modified, it had been unclear until now how oxygen molecules make their way through the enzyme. With the help of computer simulations using NAMD, researchers have identified in a recent publication, the routes taken by oxygen inside various copper amine oxidases from different species. In order to accomplish this, they analyzed simulations of the motions of four copper amine oxidases, using the VMD analysis and visualization software, which can predict the probability of finding oxygen molecules anywhere inside the simulated proteins. This analysis found numerous oxygen conduction routes inside each copper amine oxidase, i.e., oxygen can enter the protein through many routes, as it would in a sponge. More information on finding O2 migration pathways in proteins can be found here.
Copper amine oxidase

The popular Adobe PDF document format (PDF version 1.6) now supports inclusion of 3-D geometry. The latest versions of Adobe Acrobat Reader can now display, rotate, and animate 3-D models embedded within these PDF documents. This capabilities provide a tremendous new opportunity for creating tutorials, presentations, and electronic textbooks containing 3-D models of biomolecules that can be interactively manipulated by the reader. For more information, see the short tutorial on creating 3-D PDF files with VMD

The Tachyon parallel ray tracer included with VMD has been updated with the ability to display molecules with ambient occlusion lighting. This lighting technique mimicks some of the effects that occur under conditions of omnidirectional diffuse illumination, e.g. outdoors on an overcast day. This lighting used in concert with traditional point source lights and directional lights to increase the perception of shape and depth in images of molecular structures, and decreases the deleterious effects of harsh shadows which otherwise occur with lighting based on a small number of direct light sources. This lighting model is particularly good at emulating the appearance of chalky materials, and can make molecular graphics more understandable, not to mention aesthetically appealing. A short tutorial is available on using these new lighting and shading features with VMD, along with a number of representative example images. .

"I would add that VMD (and similar tools, if they yet exist) will become a primary platform upon which to study a wide range of biological problems in the future. VMD adds a new dimension to the biologist's thinking. Certain thoughts generated in interaction with VMD images are inconceivable otherwise; the `language' essential to generating these ideas would just not be there! In other words, VMD is far from a simple `visualization tool' for a biologist, it is a true thinking tool. Without it a whole class of biological hypotheses would simply not exist."
-- Carl Woese

VMD supports user-defined material and shading properties that can be used to render molecular graphics in a more illustrative style. Future versions of VMD will expand on this capability through increased use of programmable shading technology. This will bring many molecular rendering features previously found only in batch mode software renderers into the realm of interactive molecular visualization.

VMD includes a multiple sequence alignment plugin, a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids. Special emphasis is placed on analyzing the data within the framework of evolutionary biology. A paper describing MultiSeq has been published in BMC Bioinformatics

VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow huge simulation trajectories to be loaded into physical memory and accomodate large volumetric datasets. This 1,000,000+ atom Satellite Tobacco Mosaic Virus simulation is an example of the size simulation trajectory that one can analyze and display with VMD on an appropriately equipped graphics workstation.

VMD includes a plugin for creating and running APBS electrostatics calculations and can display the resulting ouput including potential maps, solvent accessibility maps, and other data produced by the APBS job. Recent versions of VMD also have the ability to run APBS jobs on remote clusters or supercomputers for fast turnaround of high resolution potential calculation needed for visualization and analysis.

VMD can load and display volumetric data sets, including electron density maps, electron orbitals, potential maps, and various types of user-generated volumetric data. The VMD plugin library contains support for a large number of volumetric file formats. Users can also import their own data file formats by writing their own loader scripts using the "mol volume" command. Volumetric data can be rendered using "VolumeSlice" or "Isosurface" representations, each of which provides several geometric rendering styles for viewing the data, varying isolevels, slice plane position, etc.

VMD includes a Virtual DNA Viewer plugin which can be used to render images of chromatin using ideal DNA interbasepair helical parameters (in proper r.h.s. ref. frame ordering). This plugin is useful for investigating the folding of chromatin based on the "two-angle" model where the total linker length and twist between nucleosomes determines the overall geometry of chromatin. This is an example of the type of visualizations that can be done with VMD using mathematical models and equations rather than all-atom structure data.

VMD can be used to display the results of HOLE calculations. HOLE calculates pore dimensions of the holes through molecular structures of ion channels. This is one of many examples of how third party packages can make use of the visualization capabilties of VMD.

Recent improvements to the data structures and algorithms used to display and analyze molecular structures in VMD have improved it's utility in bionanotechnology, and materials science where large structures, various types of non-biological matter, and non-polymeric structural elements are often present.

Dr. Oliver Beckstein's VMD image was voted "highly commended" in the 2005 Visions of Science Photographic Awards. The image illustrates the nicotinic acetylcholine receptor. The image was created by loading the crystal structure of the receptor and water density on a 3D grid into VMD 1.8.3 and rendered with Raster3D 2.7c.

VMD provides the ability to render molecular scenes using external programs such as ray tracers and commercial animation packages. This feature can be used to attain higher image quality than is normally possible using the built-in OpenGL rendering features in VMD. The Tachyon parallel ray tracer is distributed with VMD.

VMD was used to make the winning image in the Illustration category of the 2004 Visualization Challenge in Science and Engineering hosted by the National Science Foundation. The structure was loaded and visualized with VMD and the final high resolution figure was exported using the "Render" menu in VMD, and rendered using the Tachyon multiprocessor ray tracer.

VMD can display solvent-exluded molecular surfaces through the use of the program MSMS. MSMS provides VMD with fast surface calculation and display, and VMD uses high-performance display algorithms to allow large or complex surfaces to be drawn at interactive rates.

VMD can now make movies easier than ever before, with the use of a movie plugin that takes care of the entire movie making process. The vmdmovie plugin generates one of several built-in movie types, according to user selectable options. Once preferences and selections are made, the movie generator takes control of VMD and takes care of the entire process, from the generation of individual movie frames using on-screen snapshots or ray tracers, image format conversion staging of the image data for compression, invocation of movie compressor programs, and final disk space cleanup and temporary file deletion. This makes the whole process of making movies much simpler for inexperienced users.

VMD can load and display the results of ab initio simulations done with packages such as CPMD, GAMESS, Gaussian, ESPRESSO/PWScf, and others. An excellent tutorial on using VMD with these packages is available here.

VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow huge simulation trajectories to be loaded into physical memory and accomodate large volumetric datasets. This 400,000 atom virus structure is just a simple example of what can be done with VMD on an appropriately equipped graphics workstation.

VMD is frequently used to make figures and illustrations that grace the cover pages of textbooks and journals. A sampling of some of the VMD cover page images produced by local researchers and collaborators can be viewed here.

VMD includes a Ramachandran plot plugin which plots Phi and Psi angles for a selected molecule. The angle plot automatically updates when simulation trajectory frames are advanced by hand, or when animated. Each plotted angle is individually selectable, and reports its segment ID, residue name, residue ID, Phi angle, and Psi angle, when selected. Ramachandran plots can be saved to a postscript file for inclusion into publications.

VMD can be used with 3-D printers to create solid models of molecular structures such as the LH-II heterodimer unit shown at right. The most recent version of VMD supports the newest color-capable 3-D printers, and can generate STL or VRML files suitable for 3-D printing. Two identical LH-II heterodimer units were printed in 6.4 hours on a Z-Corp Z400 3-D printer at an approximate cost of $1 to $2 per cubic inch. Each of the two solid models consumed 12.4 cubic inches of the ZP102 powder.

VMD provides user-editable "materials" which can be applied to molecular geometry. These material properties control the details of how VMD shades the molecular geometry, and how transparent or opaque the displayed molecular geometry is. With this feature, one can easily create nice looking transparent surfaces which allow inner structural details to be seen within a large molecular structure. The material controls can be particularly helpful when rendering molecular scenes using external ray tracers, each of which typically differ slightly.

VMD provides a sequence plugin which can be used to view a structure's sequence, secondary structure code, and B value in a scrolling window. The sequence viewer can zoom in on a region of interest, and selections can be made on the sequence, which are then highlighted on the structure in VMD's OpenGL graphics window.

VMD takes advantage of inexpensive game technologies, graphics boards and stereo glasses to provide capabilities for PC users which were once only available in $40,000 workstations. For only a few hundred dollars, it is now possible to equip most desktop PC's with stereoscopic display capabilities, hardware accelerated 3-D rendering, and six-degree-of-freedom motion control capability.

VMD supports the use of separate displays for its graphical user interface forms and menus, and its 3-D graphics display window. This allows VMD to be used easily in a theatre or auditorium environment where one display channel may be projected on a large screen for classes or presentations, and other screens are only seen by the presenter or helpers. This feature lets the presenter show just the VMD graphics window on the projection system, without distracting the audience with other user interfaces, menus, etc.

BioCoRE enhances VMD by making it very easy to share molecular views with collaborators. Once you have a desired view in VMD, the view can be saved back to BioCoRE by selecting an option in a special BioCoRE window. Collaborators can then use BioCoRE to load the same view in their own copy of VMD.

VMD includes built-in support for IMD (Interactive Molecular Dynamics) simulations using NAMD, or Protomol. IMD allows a researcher to interact with molecular structures within a running simulation, applying forces on groups of atoms in the simulation. The user experiences force feedback when resistance is encountered, through the use of 3-D motion control devices with haptic feedback. IMD techniques are currently being applied to studies of the Glycerol channel.

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.

VMD can be used with tiled displays and cluster-based rendering systems for relatively low-cost, high resolution display of molecular geometry. This feature is particularly attractive for institutions with tiled display systems used for auditoriums, or other large-format presentation rooms. The image at the right shows a six projector tiled display at NCSA, running VMD.

VMD supports the use of six-degree-of-freedom motion control devices such as the Spaceball and Magellan. These input devices provide an easy-to-use interface for performing complex 3-D manipulation, and leave your other hand free to use the mouse and keyboard at the same time. These devices can also be used to manipulate 3-D pointers in the scene for meetings and presentations.

VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow large-size and long-timescale simulation trajectories to be loaded into physical memory and accommodate large volumetric datasets. The 64 million atom HIV capsid simulation described in the May 30, 2013 issue of Nature is a first-class example of what can be done with VMD on an appropriately equipped graphics workstation. The HIV-1 model was prepared for simulation using the structure building tools and scripting features of VMD were later used for trajectory analysis. The all-atom structure of the HIV-1 capsid shown on the Nature cover was rendered within VMD using the internal Tachyon ray tracing engine, and was then composited with an artistic representation of the viral envelope and the Nature cover text.

VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow large-size and long-timescale simulation trajectories to be loaded into physical memory and accommodate large volumetric datasets. The 64 million atom HIV capsid simulation described in the May 30, 2013 issue of Nature is a first-class example of what can be done with VMD on an appropriately equipped graphics workstation. The HIV-1 model was prepared for simulation using the structure building tools and scripting features of VMD were later used for trajectory analysis. The all-atom structure of the HIV-1 capsid shown on the Nature cover was rendered within VMD using the internal Tachyon ray tracing engine, and was then composited with an artistic representation of the viral envelope and the Nature cover text.

VMD is capable of working with very large structures up to the limits of available memory. The 64-bit versions of VMD allow large-size and long-timescale simulation trajectories to be loaded into physical memory and accommodate large volumetric datasets. The 64 million atom HIV capsid simulation described in the May 30, 2013 issue of Nature is a first-class example of what can be done with VMD on an appropriately equipped graphics workstation. The HIV-1 model was prepared for simulation using the structure building tools and scripting features of VMD were later used for trajectory analysis. The all-atom structure of the HIV-1 capsid shown on the Nature cover was rendered within VMD using the internal Tachyon ray tracing engine, and was then composited with an artistic representation of the viral envelope and the Nature cover text.

Human immunodeficiency virus type 1 (HIV-1) is the major cause of AIDS, for which treatments need to be developed continuously as the virus becomes quickly resistant to new drugs. When the virus infects a human cell it releases into the cell its capsid, a closed, stable container protecting the viral genetic material. However, interaction with the cell triggers at some point an instability of the capsid, leading to a well timed release of the genetic material that merges then with the cell's genes and begins to control the cell. The dual role of the capsid, to be functionally both stable and unstable, makes it in principle an ideal target for antiviral drugs and, in fact, treatments of other viral infections successfully target the respective capsids. The size of the HIV-1 capsid (about 1,300 proteins), and its irregular shape had prevented so far the resolution of a full capsid atomic-level structure. However, in a tour de force effort, groups of experimental and computational scientists have now resolved the capsid's chemical structure (deposited to the protein data bank under the accession codes 3J3Q and 3J3Y). As reported recently (see also journal cover), the researchers combined NMR structure analysis, electron microscopy and data-guided molecular dynamics simulations utilizing VMD to prepare and analyze simulations performed using NAMD on one of the most powerful computers worldwide, Blue Waters, to obtain and characterize the HIV-1 capsid. The discovery can guide now the design of novel drugs for enhanced antiviral therapy. More information is available on our virus website, in video, and in a press release.
HIV-1 Capsid

See also movie: 15.5MB
made with VMD


Human immunodeficiency virus type 1 (HIV-1) is the major cause of AIDS, for which treatments need to be developed continuously as the virus becomes quickly resistant to new drugs. When the virus infects a human cell it releases into the cell its capsid, a closed, stable container protecting the viral genetic material. However, interaction with the cell triggers at some point an instability of the capsid, leading to a well timed release of the genetic material that merges then with the cell's genes and begins to control the cell. The dual role of the capsid, to be functionally both stable and unstable, makes it in principle an ideal target for antiviral drugs and, in fact, treatments of other viral infections successfully target the respective capsids. The size of the HIV-1 capsid (about 1,300 proteins), and its irregular shape had prevented so far the resolution of a full capsid atomic-level structure. However, in a tour de force effort, groups of experimental and computational scientists have now resolved the capsid's chemical structure (deposited to the protein data bank under the accession codes 3J3Q and 3J3Y). As reported recently (see also journal cover), the researchers combined NMR structure analysis, electron microscopy and data-guided molecular dynamics simulations utilizing VMD to prepare and analyze simulations performed using NAMD on one of the most powerful computers worldwide, Blue Waters, to obtain and characterize the HIV-1 capsid. The discovery can guide now the design of novel drugs for enhanced antiviral therapy. More information is available on our virus website, in video, and in a press release.
HIV-1 Capsid

See also movie: 15.5MB
made with VMD


Human immunodeficiency virus type 1 (HIV-1) is the major cause of AIDS, for which treatments need to be developed continuously as the virus becomes quickly resistant to new drugs. When the virus infects a human cell it releases into the cell its capsid, a closed, stable container protecting the viral genetic material. However, interaction with the cell triggers at some point an instability of the capsid, leading to a well timed release of the genetic material that merges then with the cell's genes and begins to control the cell. The dual role of the capsid, to be functionally both stable and unstable, makes it in principle an ideal target for antiviral drugs and, in fact, treatments of other viral infections successfully target the respective capsids. The size of the HIV-1 capsid (about 1,300 proteins), and its irregular shape had prevented so far the resolution of a full capsid atomic-level structure. However, in a tour de force effort, groups of experimental and computational scientists have now resolved the capsid's chemical structure (deposited to the protein data bank under the accession codes 3J3Q and 3J3Y). As reported recently (see also journal cover), the researchers combined NMR structure analysis, electron microscopy and data-guided molecular dynamics simulations utilizing VMD to prepare and analyze simulations performed using NAMD on one of the most powerful computers worldwide, Blue Waters, to obtain and characterize the HIV-1 capsid. The discovery can guide now the design of novel drugs for enhanced antiviral therapy. More information is available on our virus website, in video, and in a press release.
HIV-1 Capsid

See also movie: 15.5MB
made with VMD


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