Under certain kinetic or thermodynamic conditions, proteins make large conformational changes, formally called state transitions, resulting in significant changes in their chemical
or biological functions. These dynamic properties of proteins can be studied through molecular
dynamics simulation. However, in contrast to conventional dynamics simulation protocols where
an initial-value problem is solved, the simulation of transition of protein conformation can be
done by solving a boundary-value problem, with the beginning and ending states of the protein
as the boundary conditions. While a boundary-value problem is generally more difficult to solve,
it provides a more realistic model for transition of protein conformation and has certain computational
advantages as well, especially for long-time simulations. Here we study the solution of the
boundary-value problems for the simulation of transition of protein conformation using a standard
class of numerical methods called the multiple shooting methods. We describe the methods and
discuss the issues related to their implementations for our specific applications, including the definition
of the boundary conditions, the formation of the initial trajectories, and the convergence
of the solutions. We present the results from using the multiple shooting methods for the study
of the conformational transition of a small molecular cluster and an alanine dipeptide, and show
the potential extension of the methods to larger biomolecular systems.