Applicability of Optimal Protocols and the Jarzynski Equality

The Jarzynski equality is a well-known and widely used identity, relating the free energy difference between two states of a system to the work done over some arbitrary, nonequilibrium transformation between the two states. Despite being valid for both stochastic and deterministic systems, we show that the optimal transformation protocol for the deterministic case seems to differ from that predicated from an analysis of the stochastic dynamics. In addition, it is shown that for certain situations, more dissipative processes can sometimes lead to better numerical results for the free energy differences.