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1 The Computational Microscope Computational microscope views at atomic resolution... Rs E M RER SER N RER C GA L... how living cells maintain health and battle disease John%Stone Our Microscope is Made of... Chemistry NAMD Software Virus ns/day cores Physics Math (repeat one billion times = microsecond)..and Supercomputers
2 NAMD impact is broad and deep 3 Comprehensive, industrial-quality software Integrated with VMD for simulation setup and analysis Portable extensibility through Tcl scripts (also used in VMD) Consistent user experience from laptop to supercomputer Large user base 51,000 registered users 9,0 (18%) are NIH-funded; many in other countries 14,0 have downloaded more than one version Leading-edge simulations most-used software on NICS Cray XT5 (largest NSF machine) by far the most used MD package at TACC (2 nd and 3 rd largest) NCSA Blue Waters early science projects and acceptance test Argonne Blue Gene/Q early science project BTRC for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC Outside researchers choose NAMD and succeed Corringer, et al., Nature, external citations since 2007 Voth, et al., PNAS, K-atom 30 ns study of anesthetic binding to bacterial ligand-gated ion channel provided complementary interpretations that could not have been deduced from the static structure alone. Bound Propofol Anesthetic 500K-atom 500 ns investigation of effect of actin depolymerization factor/cofilin on mechanical properties and conformational dynamics of actin filament. Recent NAMD Simulations in Nature Bare actin Cofilactin M. Koeksal, et al., Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis. (2011) C.-C. Su, et al., Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli. (2011) D. Slade, et al., The structure and catalytic mechanism of a poly(adp-ribose) glycohydrolase. (2011) F. Rose, et al., Mechanism of copper(ii)-induced misfolding of Parkinson s disease protein. (2011) L. G. Cuello, et al., Structural basis for the coupling between activation and inactivation gates in K(+) channels. (20) S. Dang, et al.,, Structure of a fucose transporter in an outward-open conformation. (20) F. Long, et al., Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport. (20) R. H. P. Law, et al., The structural basis for membrane binding and pore formation by lymphocyte perforin. (20) P. Dalhaimer and T. D. Pollard, Molecular Dynamics Simulations of Arp2/3 Complex Activation. (20) J. A. Tainer, et al., Recognition of the Ring-Opened State of Proliferating Cell Nuclear Antigen by Replication Factor C Promotes Eukaryotic Clamp-Loading. (20) D. Krepkiy, et al.,, Structure and hydration of membranes embedded with voltage-sensing domains. (2009) N. Yeung, et al.,, Rational design of a structural and functional nitric oxide reductase. (2009) Z. Xia, et al., Recognition Mechanism of sirna BTRC by for Viral Macromolecular p19 Suppressor Modeling of and RNA Bioinformatics Silencing: A Molecular Dynamics Study. (2009) Beckman Institute, UIUC
3 The Molecular Dynamics Simulation Process For textbooks see: M.P. Allen and D.J. Tildesley. Computer Simulation of Liquids.Oxford University Press, New York, D. Frenkel and B. Smit. Understanding Molecular Simulations. From Algorithms to Applications. Academic Press, San Diego, California, A. R. Leach. Molecular Modelling. Principles and Applications.Addison Wesley Longman, Essex, England, More at Energy function: Classical Dynamics at 300K used to determine the force on each atom: yields a set of 3N coupled 2 nd -order differential equations that can be propagated forward (or backward) in time. Initial coordinates obtained from crystal structure, velocities taken at random from Boltzmann distribution. Maintain appropriate temperature by adjusting velocities.
4 Classical Dynamics discretization in time for computing Use positions and accelerations at time t and the positions from time t-δt to calculate new positions at time t+δt. + Verlet algorithm Potential Energy Function of Biopolymer Simple, fixed algebraic form for every type of interaction. Variable parameters depend on types of atoms involved. heuristic from physics
5 Improving the Force Field Atomic polarizability increases computation by 2x but, the additional computations are perfectly suited to the GPU! For now, NAMD calculates atomic polarizability on CPUs only...soon we will also use GPUs Atomic polarizability of water, highly accurately simulated through additional particles (shown in green) NAMD CPU performance scaling polarizable water non-polarizable water Seconds per step CPU cores Molecular Dynamics Ensembles Constant energy, constant number of particles (NE) Constant energy, constant volume (NVE) Constant temperature, constant volume (NVT) Constant temperature, constant pressure (NPT) Choose the ensemble that best fits your system and start the simulations, but use NE to check on accuracy of the simulation.
6 Langevin Dynamics for temperature control Langevin dynamics deals with each atom separately, balancing a small friction term with Gaussian noise to control temperature: Langevin Dynamics for pressure control Underlying Langevin-Hoover barostat equation for all atoms: Equations solved numerically in NAMD d - dimension
7 Atom Count Principal Investigator/Program Director (Last, First, Middle): Schulten, Klaus J TR&D 1: NAMD 5 L Figure 2.2: The size of biomolecular systems that can be studied using all-atom MD simulations has steadily increased from that of Lysozyme (40,000 atoms) in 1990 to the million-atom STMV virus capsid in 2006, and now 0 million atoms as in the spherical chromatophore model shown above. Atom counts include aqueous solvent, not shown. ns/day dard mpiexec program to simplify launching NAMD within the cluster s batch environment. In NAMD#Increases#Biological#Realism#Towards#the#Cell#Scale addition, NAMD provides cross-platform extensibility through Tcl scripting, a language users are 1ms 1s 1hr 1ns 1µs 1min familiar with from its use in VMD, allowing custom simulation protocols to be implemented without recompiling the program. So prized is thetime usability scaleof NAMD that its commands, input formats, cell and Tcl interface are reproduced (as allowed ribosome by the NAMD open-source license) in the (closedsource) GPU-based ACEMD software [8], providing NAMD users with an alternate MD engine electron/atom for, e.g., studies of protein-ligand binding [9]. Significant parallel computing resources are available to NAMD users. The most popular platprotein folding form is small Linux clusters (less than 0 nodes), used by 48% of survey respondents, followed by virus Length scale 26% using large clusters (including supercomputers), and a significant minority of 4% each using NAMD on Cray or IBM Blue Gene supercomputers. is maintained by the Center on the 1nm nm NAMD 0nm 1µm 1Å machines of the NSF supercomputer centers, on which NAMD users receive significant allocations. NAMD is the most Jaguar used software on the largest NSF-funded supercomputer, representing 9% of total usage on thebluewaters 112,896-core Cray XT5 of the National Institute for Computational Sciences (see NICS letter), and by far the most used molecular dynamics package at the Texas Advanced Computing Center (see TACC letter), which hosts the second and third largest 12#ns#/#day#with#GPU#accelera5on NSF machines The Center2.000 has long been an early adopter and advocate of low-cost commodity computing techcodes:'namd/vmd'260,000'registered' nology, acquiring and using networks of workstations in 1993, Linux clusters in 1998, and graphics users,'same'user'interface'from'laptop'to' processors since 2007 [5]. Graphics processor acceleration is now ranked the most important area of BW,'busiest'code'NSF'centers future development 0 by NAMD users, an amazing reversal from 2006 in which hardware acceleration was ranked last. NAMD o oads the most time-consuming operations to NVIDIA GPUs while prenumber of Cores 0 M atom simulation PHS 398 (Rev. 06/2009) Page 249 Continuation Format Page
8 NAMD Scalability protein in neural membrane ns/day.0000 virus capsid number'of'cores From,000 to 0,000 Atom MD in k atom MD reached in 2000 then a factor increase in computation; needed to describe membrane processes; was achieved through cluster computing; produced good quality results for aquaporin; is now standard. E.Tajkhorshid, P. Nollert, M. Jensen, L. Miercke, J. O'Connell, and K. Schulten. Science, 296: , ,000 atoms, 12 ns F. Khalili-Araghi, V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophysical Journal, 98: , ,000 atoms, 0.5 µs
9 From#0,000#to#64,000,000#Atom#MD#Now allhatom#structure#of#mature#hiv#capsid 216#hexamers#+12#pentamers,#pdb#3J3Q# 64#million#atoms#total run#on#2000#crayhxk#nodes#(gpu#accelerated)#at#12#ns#/#day AllHatom#MD#Simula5on#of#HIVH1#Capsid Capsid'structure'stable'without'constraints! 1#nm 216#hexamers#+12#pentamers,#pdb#3J3Q#(available#May#29) 64#million#atoms#total Over#0#ns#of#MD#on#NSF#Blue#Waters# #5000#Nodes,#160,000#cores#H#ns/day
10 1M Atom Virus on TitanDev GPU 19 5 GPU CPU Single STMV PME every 4 steps ns/day number of nodes BTRC for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC 0M Atoms on TitanDev 20 BTRC for Macromolecular Modeling and Bioinformatics Beckman Institute, UIUC
11 Tuning#a# NAMD#Run# on#blue# Waters Large is no problem. But Molecular dynamics simulation of alpha-hemolysin with about 300,000 atoms; 1 million atom simulations are routine today, 20 million atom simulations are possible. NCSA machine room
12 But long is still a problem! biomolecular timescale and timestep limits Rotation of buried sidechains Local denaturations Allosteric transitions small protein folding s ms µs steps (30 years, 2 months) 9 ( days, 2hrs) Hinge bending Rotation of surface sidechains Elastic vibrations ns ps 6 (15 min) 3 SPEED LIMIT Bond stretching Molecular dynamics timestep fs 0 δt = 1 fs (NSF center, Shaw Res.)
Our Microscope is Made of...
The Computational Microscope Computational microscope views at atomic resolution... Rs E M RER SER N RER C GA L... how living cells maintain health and battle disease John%Stone Our Microscope is Made
Our Microscope is Made of...
The Computational Microscope Computational microscope views at atomic resolution... Rs E M RER SER N RER C GA L... how living cells maintain health and battle disease John%Stone Our Microscope is Made
The Computational Microscope
The Computational Microscope Computational microscope views at atomic resolution... Rs SER RER C E M RER N GA L... how living cells maintain health and battle disease John Stone Our Microscope is Made
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