  The connection between work and changes in the Hamiltonian for a system with
a time-dependent Hamiltonian has recently been called into question, casting
doubt on the usefulness of the Jarzynski equality for calculating free energy
changes. In this paper, we discuss the relationship between two possible
definitions of free energy and show how some recent disagreements regarding the
applicability of the Jarzynski equality are the result of different authors
using different definitions of free energy. Finally, in light of the recently
raised doubts, we explicitly demonstrate that it is indeed possible to obtain
physically relevant free energy profiles from molecular pulling experiments by
using the Jarzynski equality and the results of Hummer and Szabo.
