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Simulating synthetic polymer chains in parallel

  • Bernd Jung
  • Hans-Peter Lenhof
  • Peter Müller
  • Christine Rüb
Track C1: (Industrial) End-user Applications of HPCN
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1593)

Abstract

We have investigated algorithms that are particularly suited for the parallel MD simulations of synthetic polymers. These algorithms distribute the atoms of the polymer among the processors. Dynamic non-bonded interactions, which are the difficult part of an MD simulation, are realised with the help of a special coarse-grained representation of the chain structure. We have devised and compared a master version and a distributed version of the algorithm. Surprisingly, the master version is competitive for a relatively large number of processors. We also investigated methods to improve load balancing. The resulting simulation package will be made available in the near future.

Keywords

Load Balance Synthetic Polymer Static Pair Stochastic Force Dynamic Load Balance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag 1999

Authors and Affiliations

  • Bernd Jung
    • 1
  • Hans-Peter Lenhof
    • 2
  • Peter Müller
    • 2
  • Christine Rüb
    • 2
  1. 1.Editorial Office “Macromolecular Chemistry and Physics”MainzGermany
  2. 2.Max-Planck-Institut für InformatikSaarbrückenGermany

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