PRL Abstract
Abstract
Recent advances in molecular dynamics methodology have made it
possible to study routinely the microscopic details of
chemical processes in the condensed phase using high speed computers.
Thus, it is timely and useful to provide a pedagogical treatment of the theoretical
and numerical aspects of modern molecular dynamics simulation techniques
and to show several applications that illustrate the capability of the approach.
First, the standard Newtonian or Hamiltonian dynamics based method
is presented followed by a discussion of theoretical advances related to
non-Hamiltonian molecular dynamics. Examples of non-Hamiltonian
molecular dynamics schemes capable of generating the canonical and isothermal-isobaric
ensemble are analyzed. Next, the novel Liouville operator factorization approach
to numerical integration is reviewed. The power and utility of this new technique
are contrasted to more basic methods, particularly,
in the development of multiple time scale and non-Hamiltonian integrators.
Since the results of molecular dynamics simulations depend on the
interparticle interactions employed in the calculations, modern
empirical force fields and {\it ab initio} molecular dynamics approaches are
discussed. An example calculation combining an empirical force
field and novel molecular dynamics methods, the mutant T4 lysozyme, M61,
in water, will be presented. The combination of electronic structure
with classical dynamics, the so called {\it ab initio} molecular dynamics method,
will be described and an application to the structure of
liquid ammonia is discussed. Last, it will then be shown how the classical
molecular dynamics methods can be adapted for quantum calculations
using the Feynman path integral formulation of statistical mechanics. An
application, employing both path integrals and {\it ab initio} molecular
dynamics, to an excess proton in water will be presented.