Simulating synthetic polymer chains in parallel
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.
KeywordsLoad Balance Synthetic Polymer Static Pair Stochastic Force Dynamic Load Balance
Unable to display preview. Download preview PDF.
- M. P. Allen and D. J. Tildesley. Computer simulation of liquids. Clarendon Press, Oxford, 1989.Google Scholar
- M. Forum. MPI: A message-passing interface standard. International Journal of Supercomputer Applications, 8:165–416, 1994.Google Scholar
- J. M. Haile. Molecular Dynamics Simulation. Wiley, 1992.Google Scholar
- B. Jung, H.-P. Lenhof, P. Müller, and C. Rüb. Parallel MD-simulations of synthetic polymers. In Proc. of the 8th SIAM Conference on Parallel Processing for Scientific Computing, 1997.Google Scholar
- M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kale, R. Skeel, and K. Schulten. NAMD—A parallel object-oriented molecular dynamics program. Journal of Supercomputing Applications and High Performance computing, 10:251–268, 1996. Package NAMD, http://www.ks.uiuc.edu/Research/namd/namd.html.Google Scholar
- 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, //tincan.bioc.columbia.edu/Lab/pmd/Google Scholar