PRL Abstract
Abstract
Modern Molecular Dynamics methods are employed to study quantum
manybody systems, chemically reactive systems
including explicit electronic degrees of freedom, and combinations thereof,
as well as large classical biomolecular systems.
Novel algorithms have been combined with parallelization technology
into a single unified package, PINY_MD, developed by the authors.
Thus, complex problems
such as isotope effects on enzymatic reactions can now be examined,
routinely. In this article,
modern molecular dynamics methods are reviewed and their application
to quantum manybody systems and electronic structure calculations
described. The resulting methodology, however, while powerful, is
computationally intensive. Therefore,
the mathematical structure of the techniques has been exploited to
develop distributed memory parallel
algorithms employing multiple levels of discretization.
These multilevel-parallel methods are efficient and permit the large
complex systems, such as enzyme catalysis, to be treated easily. In addition,
it is shown how modern object oriented programming paradigms can be
employed to implement multilevel parallel algorithms
in a large computational package rapidly and efficiently.
Finally, results and timings obtaining
using the PINY_MD package are given for a variety of novel systems.