Creating the Molecules of Life with HiPerGator

The University of Florida’s HiPerGator, the most powerful supercomputer in higher education, is transforming the world of molecular research.

Jinze Xue, a Ph.D. student in the Roitberg Computational Chemistry Group, recently conducted a large-scale early Earth molecular dynamics experiment using HiPerGator. The experiment utilized over 1,000 A100 GPUs on 22 million atoms to discover how complex molecules can form from the basic building blocks of life and to make the process automatic through large-scale computer simulations.

Adrian Roitberg, Ph.D., a professor in the UF Department of Chemistry and leader of the Roitberg Computational Chemistry Group, said HiPerGator allows the team to perform calculations that were impossible just a few years ago.

“Our previous success enabled us to use Machine Learning and AI to calculate energies and forces on molecular systems, with results that are identical to those of high-level quantum chemistry but around 1 million times faster,” said Roitberg. “These questions have been asked before but, due to computational limitations, previous calculations used small numbers of atoms and could not explore the range of time needed to obtain results. But with HiPerGator, we can do it.” 

The emergence of AI and incredibly powerful GPUs has given HiPerGator the ability to perform large ‘hero’ calculations that use the entire machine, making what was previously a dream for researchers into a reality.

“Using Machine Learning methods, we created a simulation using the complete HiPerGator set of GPUs,” Roitberg said. “We were able to see, in real time, the formations of almost every amino acid (alanine, glycine, etc.) and a number of very complex molecules. This was very exciting to experience.” 

Read more: Creating the Molecules of Life with HiPerGator.