Point-centered domain decomposition for parallel molecular dynamics simulation Original Research Article

A new algorithm for molecular dynamics simulations of biological macromolecules on parallel computers, point-centered domain decomposition, is introduced. The molecular system is divided into clusters that are assigned to individual processors. Each cluster is characterized by a center point and comprises all atoms that are closer to its center point than to the center point of any other cluster. The point-centered domain decomposition algorithm is implemented in the new program Opalp using a standard message passing library, so that it runs on both shared memory and massively parallel distributed memory computers. Benchmarks show that the program makes efficient use of up to 100 and more processors for realistic systems of a protein in water comprising 10000 to 20000 atoms.