![]() Molecular visualization tool capable of achieving smooth animations The conventional Surf and MSMS representations, and makes VMD the first Representation in VMD achieves performance orders of magnitude faster than ![]() Recently, we have developed a new GPU-accelerated multi-resolutionĮnabling smooth interactive animation of moderate sized biomolecularĬomplexes consisting of a few hundred thousand to one million atoms,Īnd interactive display of molecular surfaces for multi-million atomĬomplexes, e.g. Structures are exposed to solvent, where structuresĬome into contact, and to view the overall architecture of largeīiomolecular complexes such as trans-membrane channels and virus capsids. Molecular surface visualization allows researchers to see where These and other CPU-bound operations must be ported to the GPU beforeįurther acceleration of the entire NAMD application can be realized. With bonded forces and PME long-range force calculations on the CPU. The twenty-fold acceleration provided by the GPU decreases the runtimeįor the non-bonded force evaluations such that it can be overlapped The high degree of parallelism and floating point arithmeticĬapability of GPUs can attain performance levels twenty times Molecular dynamics simulation is the evaluation ofįorces between atoms that do not share bonds. ![]() One of the most time consuming calculations in a typical Simulation techniques for accelerating processes of interest. Requires simulations of 100 ns or longer, even when employing Studying the function of even the simplest biomolecular machines NAMD simulations have exceeded 10,000,000 atoms. Such systems routinely comprise 100,000 atoms, and several published Proteins in solvent to complex aggregates, often in a lipid environment. Rapidly expanded the domain of biomolecular simulation from isolated Theĭiscovery can guide now the design of novel drugs for enhancedĬontinuing increases in high performance computing technology have Waters, to obtain and characterize the HIV-1 capsid. NAMD on one of the most powerful computers Researchers combined NMR structure analysis, electron microscopy and However, in a tour de forceĪnd computational scientists have now resolved the capsid'sĬhemical structure (deposited to the protein data bank under the Proteins), and its irregular shape had prevented so far the resolution The size of the HIV-1 capsid (about 1,300 Treatments of other viral infections successfully target the It in principle an ideal target for antiviral drugs and, in fact, Role of the capsid, to be functionally both stable and unstable, makes Then with the cell's genes and begins to control the cell. Leading to a well timed release of the genetic material that merges With the cell triggers at some point an instability of the capsid, ![]() When the virus infectsĪ human cell it releases into the cell its capsid, a closed, stableĬontainer protecting the viral genetic material. Virus becomes quickly resistant to new drugs. Human immunodeficiency virus type 1 (HIV-1) is the major cause ofĪIDS, for which treatments need to be developed continuously as the GPU Calculation of All-Atom HIV-1 Structureīlue Waters GPU-accelerated SupercomputerĮlusive HIV-1 Capsid Structure Determination Accelerated by GPUs.Several exemplary results from our GPU computing work are presented in Many molecular modeling applications are well suited to GPUs, due to theirĮxtensive computational requirements, and because they lend themselves to That scale to hundreds of tightly coupled processing units. The design and implementation of data-parallel algorithms The increased capabilities and flexibility of recent GPU hardwareĬombined with high level GPU programming languages such asĬUDA and OpenCL has unlocked this computational power and made it Numerically intensive scientific applications such as molecular modeling. Units and can be harnessed to provide tremendous acceleration for Modern graphics processing units (GPUs) contain hundreds of arithmetic
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