Point-centered domain decomposition for parallel molecular dynamics simulation

A new algorithm for molecular dynamics simulations of biological macromolec ules on parallel computers, point-centered domain decomposition, is introdu ced. The molecular system is divided into clusters that are assigned to ind ividual processors, Each cluster is characterized by a center point and com prises all atoms that are closer to its center point than to the center poi nt of any other cluster. The point-centered domain decomposition algorithm is implemented in the new program OPALP using a standard message passing li brary, so that it runs on both shared memory and massively parallel distrib uted memory computers. Benchmarks show that the program makes efficient use of up to 100 and more processors for realistic systems of a protein in wat er comprising 10 000 to 20 000 atoms. (C) 2000 Elsevier Science B.V. All ri ghts reserved.