Computing, high performance

Herein lie two fairly different approaches to this problem. One approach considers the computational tractability to be paramount, and in this case, one is willing to sacrifice accuracy for tractability. Protein-ligand docking is an example of this approach, and due to its tractability, has become a very prevalent means to quickly assay how well a ligand can bind to a protein. 

The opposite approach has also been considered to make accuracy paramount, independent of computational cost. For example, these cases typically employ the most accurate methods and complex sampling methods, both of which contribute to the computational complexity of the calculation. Clearly, just because a calculation is computationally demanding does not in itself demonstrate that it will be more accurate. However, elements which contribute to the accuracy of a calculation in terms of more accurate models — e.g., all-atom models, explicit solvation — or enhancing the degree of sampling would clearly be more computationally demanding. 

To examine the accuracy of solvation free energies, first one needs to achieve a sufficient precision to compare with experiment. This was recently done extensively by Shirts et al. [101], where the Folding0Home distributed computing network 

1 Enhancing Sampling A Natural Role for High-Performance Computing 

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By using modern high-performance computers, it has become possible to present the test data planiform. That way, for the first time a direct relation between the test signals and the test item could be achieved. 

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L., Skeel, R.D., Schul-ten, K. NAMD - A parallel, object-oriented molecular dynamics program. Int. J. Supercomputing Applications and High Performance Computing 10 (1996) 251-268. 

J. F. Leathrum, Jr. Scalable implementations of multipole-accelerated algorithms for molecular dynamics. In Proceedings of the Scalable High-Performance Computing Conference, pages 87-94, Los Alamitos, Calif., 1994. IEEE Computer Society Press. 

K. Schulten. NAMD—a parallel, object-oriented molecular dynamics program. Inti. J. Supercomput. Applies. High Performance Computing, 10 251-268, 1996. 

Clark, T., Hanxleden, R., McCammon, J., Scott, L. Parallelizing molecular dynamics using spatial decomposition. In Proceedings of the scalable high performance computing conference. May 23-25, 1994, Knoxville, Tennessee. IEEE Computer Society Press, Los Alamitos, California, 1994. 

B. Rau and co-wotkets, IEEE Computer 1989). Special issue devoted to design of high performance computers. 

Another way of going further is connected with re-ordering of these groups in reverse direction or inserting k = 1 and m = 1 in all of the iterations. The separate elimination method may be of assistance in minimizing the total volume of the available information in the storage of high-performance computers. 

Scott RK. Assessing the impact of high-performance computing on the drug discovery and development process. Drug Discovery Today 2004 2 175-9. 

Predictive biosimulation is the use of computer modeling to put all the pieces of the biological puzzle together in a dynamic model that shows how they interact and work as a whole (see Chapters 6 and 22). It goes hand in hand with high-performance computing because it requires enormous computing resources. 

Computer resources and support were provided by the Large Allocations Resource Committee through grant TG-MCA05S010 and the University of Florida High-Performance Computing Center.Amber developers team, TG allocation. 

One of the authors (ML) is grateful to Fukui Institute for Fundamental Chemistry, Kyoto University for a Fukui Institute Fellowship. The present work was in part supported by a CREST (Core Research for Evolutional Science and Technology) grant in the Area of High Performance Computing for Multi-scale and Multi-physics Phenomena from the Japan Science and Technology Agency (JST). 

Violi A, Voth GA (2005) In High Performance Computing and Communications, Proceedings, pp 938-947... 

Mertz JE, Pettitt BM (1994) Molecular dynamics at a constant pH. Int J Supercomput Appl High Perform Comput 8 47-53. 

Yabe, T. Interface Capturing and Universal Solution of Solid, Liquid and Gas by CIP Method . Proceedings of the High-Performance Computing of Multi-Phase Flow, Tokyo, July 18-19, 1997. 

Derksen, J. J., Kooman, J. L., and Van den Akker, H. E. A., Parallel flow simulations by means of a lattice-Boltzmann scheme , In B. Hertzberger, P. Sloot (Eds.), High-Performance Computing and Networking , Lecture Notes in Computer Science 1225, 524-530 (1997). 

R. R. Brooks, C. Griffin, and D. S. Friedlander, Self-organized distributed sensor network entity tracking , International Journal of High Performance Computing Applications, Vol. 16, No. 3, pp. 207-219, August 2002. 

High Performance Computing in Computational Chemistry Methods and Machines. 

Modern laboratories are complex multifaceted units with vast amounts of information passing to and from instruments and computers and to and from analysts and clients daily. The development of highspeed, high-performance computers has provided laboratory personnel with the means to handle the situation with relative ease. Software written for this purpose has meant that ordinary personal computers can handle the chores. The hardware and software system required has come to be known as the laboratory information management system (LIMS). 

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