Saturday, April 19, 2025
4/19/2025
Breakthrough Molecular Dynamics Research via an Anton2 Supercomputer - Project Summary In 2010, Pittsburgh Supercomputing Center (PSC) and D.E. Shaw Research (DESRES) partnered to make the Anton special-purpose molecular dynamics (MD) supercomputer available to the national biomedical research community for the first time. Anton enabled researchers to simulate biomolecular systems two orders of magnitude faster than any conventional supercomputer, allowing researchers access to critical multi- microsecond and longer timescales on which most biologically-significant molecular processes take place. In 2016, with operational support from NIH, DESRES made available a next generation Anton 2 system at PSC at no cost. This multimillion-dollar gift from DESRES, with NIH support, provided a unique opportunity for researchers to tackle even more groundbreaking biological questions by simulating systems as large as 700,000 atoms at a rate of multiple microseconds per day. The goal of this renewal project is to provide the national biomedical research community with continued access to this unique and powerful Anton 2 resource and to maximize the benefit of this resource to the community. Since 2010, PSC has supported 589 research projects conducted by 202 unique PIs on the Anton systems hosted at PSC. So far, these projects have resulted in 292 publications, many of which have had significant impact on their fields of research. These fields cover the entire spectrum of biomolecular processes that form the fundamental underpinnings of biology, including protein folding, ion channel selectivity and gating, membrane dynamics and organization, protein- ligand binding, and many others. Demand for Anton 2 is quite high, with 2-3x higher demand than can be met each year. Given this, our goals are focused not only on providing continued access but also on maximizing the value of this limited resource to the community—recognizing that the creativity of the broad, diverse Anton 2 research community is one of our most powerful resources for innovation. Anton 2 will be integrated as an XSEDE service provider, and the accessibility and impact of Anton 2 will significantly increase by engaging in their extensive broadening participation, outreach, and training programs. Through these outreach efforts, researchers at many more institutions will have the opportunity to use Anton 2, especially researchers from traditionally underrepresented groups in biomedical research. The hundreds of long-timescale MD trajectories researchers generate on Anton 2 constitute a unique and valuable dataset that can be used to gain additional biomedical knowledge and advance the application of machine learning protocols to augment molecular dynamics simulations. This important dataset will be available to researchers and educators worldwide through a web portal and co-located on the PSC's Bridges-2 system for classroom instruction and research, including reanalysis, machine learning, and data mining.
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