  A main goal of single-molecule experiments is to evaluate equilibrium free
energy differences by applying fluctuation relations to repeated work
measurements along irreversible processes. We quantify the error that is made
in a free energy estimate by means of the Jarzynski equality when the
accumulated work expended on the whole system (including the instrument) is
erroneously replaced by the work transferred to the subsystem consisting of the
sole molecular construct. We find that the error may be as large as 100%,
depending on the number of experiments and on the bandwidth of the data
acquisition apparatus. Our theoretical estimate is validated by numerical
simulations and pulling experiments on DNA hairpins using optical tweezers.
