CUDA Spotlight: Aron Broom
GPU-Accelerated Molecular Dynamics
This week's Spotlight is on Aron Broom. Aron is a researcher at the University of Waterloo in Canada, where he works on the molecular engineering of protein structure and function.
Aron's current research interests include protein-ligand binding - particularly of a multivalent nature - and stability and symmetry in protein structure and evolution.
This interview is part of the CUDA Spotlight Series.
Q & A with Aron Broom
NVIDIA: Aron, how did you become involved in Molecular Dynamics (MD)?
Aron: I started working on protein receptor site design (the "lock") and ligand drug candidates (the "key") binding largely from an experimental perspective, but without extremely labor and resource intensive techniques, one often doesn't get a sense of what is happening at a detailed molecular level.
For instance, you can see from a "dry" crystal structure where on a protein a particular compound binds, but since these bindings occur in liquid water you don't know what kind of movements were needed to get it there, hold it there via non-bonding forces or which parts are most critical for that interaction (it's not always the parts closest to one another).
I wanted to know what was happening at a molecular level. I wanted to "see" what the atoms were doing. MD was the perfect tool and GPUs make the simulations much more affordable and accessible to the "common man."
NVIDIA: Give us a quick description of MD.
For example, MD allows scientists to study how tightly a drug compound will bind a medically relevant protein or other target (carbohydrate, nucleic acid, or lipid). But more importantly, the high level of detail allows us to understand and subsequently redesign a better drug candidate for that existing binding site.
MD simulations often involve thousands to millions of atoms, all interacting with one another through several different forces. But simply computing these interactions once only gives a single snapshot. In order to understand the dynamics and properties of the molecules of interest we must repeat these large calculations millions, billions or even trillions of times; GPUs have been most helpful in that we can now simulate larger systems for the longer timeframes needed to see the final equilibrium state obtained.
NVIDIA: What are some key challenges in your field?
Furthermore, in order to accurately calculate the properties I'm interested in, not only does each individual simulation need to be long enough to capture the relevant configurations of the molecules involved, but it is often necessary to run multiple simulations, each of which examines the behavior of the molecules under different conditions and to statistically analyze these multiple independent "movies" to see what is most likely to occur in nature.
Overall, this creates a situation in which the computational demand is extremely high, and solving the problem using CPUs would simply not be feasible under realistic conditions where large high-powered computing resources need to be shared with many other scientists. Because of the incredible performance to price and performance to power ratios of GPUs, I'm able to study problems using small GPU clusters which would not be possible using larger traditional CPU-only clusters.
NVIDIA: What are some examples of your focus areas?
NVIDIA: When does it make sense to use a single GPU workstation rather than a cluster?
For instance, implicit solvent simulations (where water is treated as a continuum rather than individual atoms) benefit to an extraordinary extent from running on a GPU. Using a single GeForce GTX570 in my desktop, I'm able to simulate protein folding and protein-protein interactions of a moderately-sized molecular system at a speed that would require ~400 CPU cores if running in NAMD (which is known for nearly linear scaling across multiple CPU cores) on a modern HPC cluster.
Given that the GTX570 itself has 480 cores, we can see that for this application a GPU and CPU compare almost core-to-core, and given that newer GPUs contain thousands of cores, the possibilities for the future are staggering.
NVIDIA: What's next on the horizon?
For instance the following molecular dynamics programs have had many or all of their components ported to a GPU version: AMBER, NAMD, LAMMPS and GROMACS. And, OpenMM is designed expressly for use on a GPU.
Given the incredible explosion in GPU performance, with the number of cores more than quadrupling over the last year alone, I expect we're quite rightfully seeing a shift to a new standard where GPU enhancement becomes the norm. Overall it's a thrilling time to be doing computational science!
Bio for Aron Broom
Starting as an experimentalist, Aron spent much of his time running around the lab with vials of purified protein. After completing a Master's in biochemistry he switched to a computational perspective and has been sitting at a computer ever since. In his ever-decreasing spare time he enjoys canoeing, rock-climbing, and any coding or electronics tinkering he can manage.