Large-scale systems of thousands and millions of atoms are of great interest in many areas of chemistry, biochemistry, and materials science. Atomic-level simulations of such systems can provide increased accuracy and especially enhanced insight and understanding when compared with either smaller-scale model calculations or grossly-averaged macroscopic models.

Megamolecular simulations require large amounts of memory and computation, far more than can be provided by the typical scientific workstation. These resources can be most cost-effectively provided at this time by scalable massively parallel computers.

This thesis presents a large-scale, parallel, distributed-memory, general-purpose molecular dynamics code. The most time-consuming portion of the calculation, the computation of the nonbonded forces, is handled by the Cell Multipole Method, which was developed to overcome the speed and accuracy limitations of standard techniques for handling long-range power-law interactions in large molecular systems. Versions of the code for the KSR-1 and Intel Delta and Paragon parallel supercomputers are described, and performance, accuracy, and scalability results are given.

The applications section begins with a discussion of computational experiments leading to a prescription for choosing the value of the free time-scale parameter in Nosé-Hoover constant-volume, constant-temperature (NVT) canonical dynamics. This is followed by several applications of the above megamolecular dynamics codes to interesting chemical applications in the areas of argon cluster structure, polymer structure, surface tension of water drops, diffusion of gases through polymers, and viral structure.

Table of Contents
Kian-Tat Lim