Parallel computations of molecular dynamics trajectories using the stochastic path approach

A novel protocol to parallelize molecular dynamics trajectories is discusse d and tested on a cluster of PCs running the NT operating system. The new t echnique does not propagate the solution in small rime steps, but uses inst ead a global optimization of a functional of the whole trajectory. The new approach is especially attractive for parallel and distributed computing an d its advantages (and disadvantages) are presented. Two numerical examples are discussed: (a) A conformational transition in a solvated dipeptide, and (b) The R --> T conformational transition in solvated hemoglobin. (C) 2000 Elsevier Science B.V. All rights reserved.