Molecular mechanical calculations on parallel and distributed processors

The molecular mechanical potential function is widely used in molecular modeling and simulation research. The most CPU time consuming parts of molecular mechanical potential are the nonbonding interaction terms. An efficient parallel algorithm for nonbonding energy calculation is outlined and its implementation is tested on a variety of parallel and distributed processing elements. As minimal parallel constructs are added, the current implementation does not modify nor slow down the serial algorithm. Load balancing, flexible enough to accommodate local loads of each PE and optimization of list updating procedure are desired and under development