Parallel MD-Simulations of Synthetic Polymers

A parallel algorithm is presented that allows efficient Langevin-dynamics simulations of single macromolecular coils which are the typical structure of synthetic polymers in solution and in bulk. Contrary to the usual spatial decomposition algorithms, we map the one-dimensional topology of the chain molecule on the parallel computer. Only short-range interactions between atoms are considered. The necessary neighbour search is done by a master-slave method

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