GPU Accelerated Apps Momentum

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1 GPU Accelerated Apps Momentum Key codes are GPU Accelerated! Molecular Dynamics Abalone GPU only code ACEMD GPU only code AMBER CHARMM DL_POLY GROMACS HOOMD-Blue GPU only code LAMMPS NAMD Quantum Chemistry ABINIT BigDFT CP2K GAMESS Gaussian in development NWChem Quantum Espresso TeraChem GPU only code VASP Check many more apps at

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3 Unveiling the structure of the HIV-1 capsid Juan R. Perilla Theoretical and Computational Biophysics Group University of Illinois at Urbana-Champaign

4 HIV Replication Cycle - Overview Source: NIAID/NIH

5 Structure of the HIV capsid Pentamers introduce sharp declinations Continuously changing curvature in the hexagonal lattice Highly schematic model; beads are not proteins! Ganser, B. K. (1999). Science, 283, Capped fullerene cone Briggs, J. et al. (2006). Structure, 14, 15 20

6 X-ray structure of CA Obtained Through Ingenious Preparation increase concentration Pornillos, O., Sønquist, et al. (2009). Cell, 137(7),

7 Structure of Full Length CA NTDs and CTDs play different roles C-terminal domain hexameric center trimeric center There are also dimeric symmetry centers! N-terminal domain hexamer Ganser-Pornillos, B. K. et al. (2007). Cell, 131(1), CA-hexameric planar lattice in crystal NTD fills inside space of hexamers, CTD fills outside.

8 Cryo-EM maps of the HIV Capsid in vitro, 1 M NaCl Cryo-EM micrograph of recombinant WT HIV-1 CA at 8 Angstrom

9 All-atoms MD of HIV-1 CA tube 71 hexamers 13 million atoms 10 ns MDFF coupled to density 125 ns MD, Blue waters NAMD Early Science System

10 NAMD Benchmarks on the Early Science System (no-gpu)

11 MDFF Structural Refinement hydrophobic interaction at trimeric interface, surr. by polar residues a view into the trimeric interface, contacts between three helices_10 formation of peripheral hydrogen bonds

12 Modeling of Pentameric Oligomers CA-Pentamer (1.3 M atoms) 1.5 µs simulation on Titan, GPU accelerated Pentamer-of-Hexamers (POH) P/H H10 H10 H10 Hexamer-of-Hexamers (HOH) H Compare: (1) H10 superimposed from HOH, (2) H10 from POH; clearly pentamer H10 moves a lot, H10(P)+H10(H)^2 become more compact than H10(H)^3 H

13 MD:HIV-1 CA pentamer-hexamer 1.3 million atoms 1.5 µs MD NAMD GPU-accelerated on NVIDIA Fermi GPU

14 Infectivity (% of WT) Core Associated CA (%) CA CTD trimer interface A204 I201 E213 K nm Gongpu Zhao A204C assembles efficiently into cones A204C cross-links only in mature virions mature CA6 WT A204C 75 WT A204C WT A204C Ernest Yufenyu & Chris Aiken WT 204C 204D 204L 204K 204Y

15 Analogy with fullerenes High correlation with experimental density The parameter ξ measures the deviation of the fullerene from a perfect sphere and the strength of its deformation. A perfect sphere corresponds to ξ=0, and an axially symmetric ellipsoid corresponds to ξ=1. Fitted structure High strain region

16 Isomer search and geometry optimization Spiral search on 2D-projection 3D-embedding DFT geometry optimization

17 Correlation 252H +12P 216H +12P 212H +12P 166H +12P Fullerene model number

18 All-atom MD simulation of mature HIV-1 capsid 216 hexamers +12 pentamers (13.4 M), 64 million atoms total including solvent 100 ns running NAMD on 4000 Cray-XE nodes, cores 6 ns/day, all-atom

19 All-atom MD simulation of mature HIV-1 capsid 186 hexamers +12 pentamers (12 M), 64 million atoms total 100 ns running NAMD on NCSA Blue Waters 2000 to 3500 XK Nodes equipped with NVIDIA Tesla K20X 9 to 12 ns/day

20 PDB Molecule of the month Paper folding model Courtesy of David Goodsell (Scripps)

21 Acknowledgments Peijun Zhang Angela M. Gronenborn Department of Structural Biology Center for HIV Protein Interactions University of Pittsburgh School of Medicine Christopher Aiken Department of Pathology, Microbiology and Immunology Vanderbilt University Medical Center

22 Acknowledgments John Stone VMD Jim Phillips NAMD Theoretical and Computational Biophysics Group University of Illinois Urbana-Champaign

23 Upcoming GTC Express Webinars July 25 - ACEMD: High-throughput Molecular Dynamics with NVIDIA Kepler GPUs July 30 - Getting Started with GPU-accelerated Computer Vision using OpenCV and CUDA July 31 - NMath Premium: GPU-accelerated Math Libraries for.net Register at

24 GTC 2014 Call for Submissions Looking for submissions in the fields of Science and research Professional graphics Mobile computing Automotive applications Game development Cloud computing Submit at

25 Test Drive K20 GPUs! Experience The Acceleration Questions? Contact us Run NAMD on Tesla K20 GPU today Devang Sachdev - NVIDIA Sign up for FREE GPU Test Drive on remotely hosted clusters Dr. Juan R. Perilla UIUC juan@ks.uiuc.edu Stream other webinars from GTC Express: