NYU Chemistry Professor Tamar Schlick and LANL Colleagues made the cover of the Journal of Computational Chemistry with the first billion atom molecular dynamics simulation. As part of the Los Alamos National Laboratory group, Schlick used a GATA 4 gene model simulated with a chromatin mesoscale modeling program to build a billion atom molecular system. The article, entitled, "Scaling Molecular Dynamics Beyond 100,000 Processor Cones for Large-Scale Biophysical Simulations" (click here to read the article) was picked up widely by the press. The list of authors includes Schlick group postdoctoral fellow Gavin Bascom.
Abstract: The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long‐range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. A novel algorithm was implemented for nonbonded interactions to increase single instruction multiple data (SIMD) performance, reducing memory usage for ultra large systems. Memory usage for neighbor searches in real‐space nonbonded interactions was reduced by approximately 80%, leading to significant speedup. Using experimental data describing physical 3D chromatin interactions, we constructed the first atomistic model of an entire gene locus (GATA4). Taken together, these developments enabled the first billion‐atom simulation of an intact biomolecular complex, achieving scaling to 65,000 processes (130,000 processor cores) with 1 ns/day performance. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
This research was supported by the National Institutes of Health and the U.S. Department of Energy.