Highlights of our Work
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Image courtesy L. Casalino. Made with VMD
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.