A. Windemuth. Advanced algorithms for molecular dynamics simulation: The program PMD. In Timothy G. Mattson, editor, Parallel Computing in Computational Chemistry, Washington, D.C., 1995. ACS Books. In press.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....is already very small for very low temperatures; e.g. for a Ca 40 Coulomb crystal at 1 K the wavelength is of order 10 m, a factor 50 100 smaller than the typical separation distance. sizes certain macroscopic properties of matter can be studied. There is a proliferation of programs for MD [4, 14, 30, 31, 32, 53, 77, 81, 86, 91, 98, 108, 110, 119, 124, 125] and several of these are robust production codes; some with scalable parallel implementations. They cover common MD problems and are excellent tools to perform simulations. However, many of the codes are legacy programs that are either poorly organized or extremely complex. One important factor ....

....dominate, since the integration is relatively cheap to carry out. Nevertheless, the terms of the sum of interactions U( x 1 ; x 2 ; x N ) are independent. Altogether, this makes MD to a certain extent inherently parallel.This has been exploited by several parallel MD programs [4, 14, 22, 23, 32, 53, 77, 81, 86, 91, 98, 110, 124, 125]. When parallelizing MD, there are two important considerations to make. First, the MD program must perform well for a small number of particles, i.e. less than 1000. There are several interests to carry out simulations with a few thousand particles over a long time scale, e.g. a protein ....

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A. Windemuth. Advanced algorithms for molecular dynamics simulation: The program PMD. In Timothy G. Mattson, editor, Parallel Computing in Computational Chemistry, Washington, D.C., 1995. ACS Books. In press.

.... 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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A. Windemuth. Advanced algorithms for molecular dynamics simulation: The program PMD. In T. G. Mattson, editor, Parallel computing in computational chemistry, pages 151--169. ACS

....the P processors a small region of the simulation domain. As illustrated in Figure 5 this is a geometric or spatial decomposition (SD) of the workload. For reasons that will be outlined below, there have been fewer implementations of short range macromolecular MD simulations using this method [7, 10, 27] than with RD approaches. The SD algorithm is outlined in Figure 6. Processor z owns the box labeled D z and will update the positions x z of the atoms in its box. To compute forces on its atoms a processor will need to know not only x z but also positions y z of atoms owned by processors whose ....

....512 processors of the Intel Delta at CalTech for a 10914 atom benchmark computation of solvated myoglobin with a 10.0 A cutoff in a uniformly filled 3 D box. Finally, Windemuth, has also implemented a novel solution to the load balancing problem for irregular shaped domains in his SD code PMD [27]. He defines one Voronoi point per processor scattered throughout the simulation domain. The domain is then tesselated so that each processor ends up owning the physical region of volume closest to its Voronoi point. By adjusting the position of the Voronoi points as the simulation progresses and ....

A. Windemuth. Advanced algorithms for molecular dynamics simulation: The program PMD. published by the American Chemical Society, 1994. In this volume.

....partitioned into short and long range portions. The short range portion involves a direct summation of pairwise interactions with near neighbors and thus can be parallelized by the methods described in this paper. The long range portion requires different strategies to efficiently parallelize [13, 33] and is beyond the scope of this paper. The most commonly used technique for parallelizing short range MD simulations of molecular systems is known as the replicated data (RD) method [31] Numerous parallel algorithms and simulations have been developed based on this approach [7, 11, 12, 18, ....

....computes forces on only the atoms in its sub domain. In the large N limit, the technique scales optimally as N=P , 2 since each processor need only acquire information from processors who own neighboring sub domains. However, SD algorithms have not been as widely used for molecular simulation [8, 9, 10, 14, 33] due to their complexity (particularly for bonded force computation) and the difficulty of achieving good load balance across processors for irregularly shaped or dynamically changing domains. We have developed a new parallel algorithm, called force decomposition (FD) which is particularly ....

A. Windemuth. Advanced algorithms for molecular dynamics simulations: The program PMD. In T. G. Mattson, editor, Parallel Computing in Computational Chemistry, page 151. American Chemical Society, 1995.

....resort is parallelisation. Over the last 10 15 years, a vast number of parallel MD simulation algorithms 1 A first release will be made available to the public in spring 1999. have been presented and some of them have been implemented and are available as more or less ready to use packages ([7, 8, 11, 2]) Almost all of them concentrate on the parallel simulation of biopolymers and very few (e.g. 8] also explicitly target at synthetic polymers. This is difficult to understand and regrettable. Synthetic polymers are increasingly penetrating all aspects of modern life and there is a huge demand ....

A. Windemuth. Advanced algorithms for molecular dynamics simulation: The program PMD. In T. G. Mattson, editor, Parallel Computing in Computational Chemistry, pages 151--168. ACS Books, 1995. Package PMD, http://tincan.bioc.columbia.edu/Lab/pmd/.

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A. Windemuth, Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD. ACS Books, 1995.

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Andreas Windemuth. Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD. ACS Books, 1995.

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Andreas Windemuth. Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD. ACS Books, 1995.

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