Simulating synthetic polymer chains in parallel ?
We have investigated algorithms that are particularly suited for the parallel molecular dynamics (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 new 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 developed two methods to improve load balancing. The resulting simulation package will be made available in the near future.
simulation polymers parallel molecular dynamics load balancing