  When a system is driven out of equilibrium by a time-dependent protocol that
modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these
paths can be used in nonequilibrium work theorems to estimate equilibrium
quantities, such as free energy differences. Here, we consider analyzing paths
generated with one protocol using another one. It is posited that analysis
protocols which minimize the lag, the difference between the nonequilibrium and
the instantaneous equilibrium densities, will reduce the dissipation of
reprocessed trajectories and lead to better free energy estimates. Indeed, when
minimal lag analysis protocols based on exactly soluble propagators or relative
entropies are applied to several test cases, substantial gains in the accuracy
and precision of estimated free energy differences are observed.
