Molecular mechanical calculations on parallel and distributedprocessors

摘要

The molecular mechanical potential function is widely used inmolecular modeling and simulation research. The most CPU time consumingparts of molecular mechanical potential are the nonbonding interactionterms. An efficient parallel algorithm for nonbonding energy calculationis outlined and its implementation is tested on a variety of paralleland distributed processing elements. As minimal parallel constructs areadded, the current implementation does not modify nor slow down theserial algorithm. Load balancing, flexible enough to accommodate localloads of each PE and optimization of list updating procedure are desiredand under development