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.
Citation
[99+JLM] Jung, B., Lenhof, H.-P., Müller, P., Rüb, C. (1999). Simulating synthetic polymer chains in parallel. In: Sloot, P., Bubak, M., Hoekstra, A., Hertzberger, B. (eds) High-Performance Computing and Networking. HPCN-Europe 1999. Lecture Notes in Computer Science, vol 1593. Springer, Berlin, Heidelberg . https://doi.org/10.1007/BFb0100561