Fast Algorithms and a Visualization Tool for Molecular Simulations

                         Zhong-Hui Duan
                     Univrsity of Michigan

Computer simulation is an important technique to study atomic-level
structures and dynamics of molecular systems.  The most time consuming
part in the simulation is the evaluation of the force field and the
potential energy due to non-bonded interactions between particles.

In this talk, I will report on an adaptive multipole algorithm for
potential energy evaluation.  In the algorithm, a tree data structure is
used, the energy is computed recursively as a sum of group-group
interactions and the interactions between distant groups are approximated
using multipole expansions. For systems with periodic boundary conditions,
I will describe a hybrid Ewald-multipole method for the evaluation of the
force field. Numerical results from different test cases, including water
systems, will be presented to demonstrate the efficiency of the proposed
methods.

I will also present a visualization tool developed for visualizing long
chain molecules.