Development of molecular dynamics programs for proteins with a parallelized Barnes-Hut tree code

We describe the design and the MPI-implementation of two parallel tree code molecular dynamics programs called MolTreC and Treecode AMBER, respectively. Both programs were developed using the parallel Barnes-Hut tree code for calculating Coulomb interactions which have been developed in earlier work. The parallel programs can rapidly calculate the Coulomb interactions of proteins in water without any cutoff approximations. They showed good speedups on distributed-memory multiprocessors and on PC clusters. MolTreC showed 111-fold speedup on SR2201 with 256 processors for the prowat benchmark of 11585 atoms. It was only 1.7-times slower than AMBER with 12A cutoff approximation.