This talk will provide an overview of recent advances in GPU-accelerated molecular simulations and the computing architectures that enable them. With the end of Moore’s law, performance improvements now depend on algorithmic innovations and specialized hardware. I will first discuss modern GPU architectures, supercomputers, and programming approaches that leverage massive parallelism for scientific computing. I will then highlight developments in Amber, a leading biomolecular simulation package used for computational drug discovery. Its molecular dynamics engine features a highly optimized CUDA implementation for Nvidia GPUs, recently extended to AMD (HIP/ROCm) and Intel (SYCL) devices, enabling simulations of systems with millions of atoms. Finally, I will present QUICK, a massively parallel quantum chemistry code for Hartree–Fock and DFT calculations with Gaussian basis functions on GPUs. QUICK performs all major computational steps—including Fock matrix construction and gradient evaluation—entirely on single or multiple GPUs, and couples efficiently with Amber for QM/MM molecular dynamics. Together, these efforts illustrate how advances in software and GPU technology are transforming molecular simulations, enabling faster and more accurate modeling of complex chemical and biological systems.
From Atoms to Algorithms: GPU Acceleration of Molecular Dynamics, DFT, and QM/MM Simulations
Remote event
Instructor
Associate Research Scientist, SDSC
Andreas Goetz is an associate research scientist at SDSC, where he leads a research group in Quantum- and AI-enabled computational Chemistry, working at the intersection of chemistry, life sciences, and scientific computing. His research draws on quantum mechanics, statistical mechanics, molecular dynamics, and machine learning approaches to enable simulations of complex molecular systems on massively parallel computer architectures. He is a contributing author to the ADF and QUICK quantum chemistry software and the AMBER software for biomolecular simulations, which are widely used in academic and industrial research. He is also co-founder of ATTMOS Inc., which develops technologies for computational drug discovery. Andreas enjoys training the next generation of scientists in software engineering and numerical simulation methods via lectures, workshops, and the supervision of interns. He is the author of over 80 scientific publications and editor of the book 'Electronic Structure Calculations on Graphics Processing Units. Before joining SDSC in 2009, Andreas performed postdoctoral research at the VU University in Amsterdam and obtained his undergraduate and Ph.D. degrees in chemistry from the Friedrich-Alexander University in Erlangen, Germany.