VMD - Visual Molecular Dynamics

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
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Spotlight

Members of the Theoretical and Computational Biophysics Group were part of a talented multi-institutional interdisciplinary team awarded at Supercomputing 2020 with the internationally recognized ACM Gordon Bell Special Prize for COVID-19 Research, described as the "Nobel Prize for high performance computing." The winning team developed a new AI-driven simulation workflow to drive 8.5M-atom simulations of the SARS CoV-2 spike protein, its interaction with the human receptor ACE2, and 305M-atom simulations of the full SARS CoV-2 virion, using NAMD on Summit, the most powerful supercomputer in the United States, operated by the Oak Ridge National Laboratory. The NAMD simulations collectively performed over one ZettaFLOP of calculation. The AI-driven workflow and weighted ensemble methods used by the team increased effective performance by orders of magnitude. VMD was used to build complete structures, prepare the simulations, analyze the results, and create all of the team's visualizations due to its unique capacity for working with extremely large biomolecular systems and diverse structure data. Due to decades of prior investment in the development of parallel molecular dynamics, ongoing technology collaborations with hardware vendors and national laboratories deploying top tier systems, and our lab's prior work to enable large all-atom simulations of viruses and other large systems of up to one-billion atoms, NAMD and VMD were well-prepared for the challenges posed by the project and its highly compressed research timeline. The team set several new high-water marks for the full virion simulation, molecular dynamics strong scaling performance, the scale of weighed ensemble accelerated sampling, and the use of AI-driven simulation for multiscale modeling. This marks the second Gordon Bell Prize for NAMD, which was also a winner in 2002. Read more about the Gordon Bell Special Prize for COVID-19 Research here.

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Image courtesy L. Casalino.
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