VMD is a molecular visualization program for displaying, animating,
and analyzing large biomolecular systems using 3-D graphics and
VMD supports computers running MacOS X, Unix, or Windows,
is distributed free of charge, and includes source code.
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.
News and Announcements
GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting, FD169, 2014.
Methodologies for the Analysis of Instantaneous Lipid Diffusion in MD Simulations of Large Membrane Systems, FD169, 2014.
Webinar: GPU-Supercharged Molecular Visualization / Analysis with VMD
2014 VMD Calendar
GPU-accelerated molecular visualization on petascale supercomputing platforms, UltraVis'13
Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters, Proc. XSCALE, 2013.
Rapid parameterization of small molecules using ffTK, JCC, 2013.
Most cited since 2008: "GPU-Accelerated Molecular Modeling Coming of Age"
VMD QuickSurf rendering of HIV-1 capsid on cover of Nature 497 (7451), 2013.
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation, J. Comp. Chem, 2013.
Force Field Toolkit (FFTK) tutorial screencasts
Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories, EuroVis 2012.
Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories, LNCS, 2011.
Gallery of Posters, Images, and Movies made with VMD
VMD running in the NanoDome at Temple University
VMD User Survey Results
VMD development status and pre-release test downloads
CVS source code access
VMD Programmer's documentation