A. Toukmaji and D. Paul and J. A. Board, Jr., Distributed Particle-Mesh Ewald: A Parallel Ewald Summation Method, Proceedings, International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'96), CSREA Press (1996), pp. 33--43.  Home/Search   Document Details and Download   Summary   Related Articles   Check

.... Kale, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten Theoretical Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, IL 61801. kale,skeel,milind,brunner,gursoy, nealk,jim,ari,krishnan,kschulte ks.uiuc.edu March 22, 1999 1 Abstract Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such ....

....atoms. Most often, the dynamics of such systems must be studied over several nanoseconds to develop significant understanding of the phenomena being studied. At the same time, the time scale of atomic interactions requires that ome simulates their behavior in time steps as small as one femtosecond (10 15 seconds) In spite of the dramatically increased speeds of individual processors, the number of computational steps required to complete relevant simulations is prohibitive on any single processor computer. Parallel computing provides the potential for making the required large scale ....

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Abdulnour Toukmaji, Daniel Paul, and John A. Board Jr. Distributed particle-mesh Ewald: A parallel Ewald summation method. In Proceedings of the Parallel and Distributed Processing Techniques and Applications Conference, Aug 9-11,

....calculations consume a small fraction of the total computation time, particularly when combined with multiple timestepping methods, but their contribution to scalability must still be addressed. The parallelization of these methods is the subject of ongoing research by ourselves and others [14, 15, 16]. The next section describes a general methodology that we are developing for e#ective parallelization of dynamic and irregular computations, and how it is supported by the Charm parallel programming system. Section 3 briefly explains the basic parallel structure and algorithm used in NAMD, ....

Abdulnour Toukmaji, Daniel Paul, and John A. Board Jr. Distributed particle-mesh Ewald: A parallel Ewald summation method. In Proceedings of the Parallel and Distributed Processing Techniques and Applications Conference, Aug 9-11, 1996, Sunnyvale, CA, 1996.

....of Hockney and Eastwood [8] to interpolate all the randomly spaced particles onto a regular mesh. The Fourier sum is then computed via FFT techniques and the results interpolated back to the actual particle sites. Our interest has been to parallelize PME; some of our efforts are described in [4]. The three dimensional FFT needed by PME is notoriously difficult to parallelize, so we first bias the work as much as possible to the real space term (essentially by increasing the cut off radius for the error function, which reduces the number of lattice vectors needed for good accuracy in the ....

A. Toukmaji and D. Paul and J. A. Board, Jr., Distributed Particle-Mesh Ewald: A Parallel Ewald Summation Method, Proceedings, International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'96), CSREA Press (1996), pp. 33--43.

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