An approach closer to the in situ modeling of the molecular electronic device is proposed with partial relaxation of the molecular geometry under the interaction of the external electric field. A typical molecular wire (4,4'-(1,4-phenylenedi-2,1-ethynediyl)bis-benzenethiol) has been studied by this methodology using first-principles DFT calculations and non-equilibrium Green's function formalism. It is found that the optimized molecular wire exhibits a different behavior compared with the geometry-frozen one. The HOMO-LUMO gaps, spatial distributions of the frontier molecular orbitals, and the transmission spectra have been used in the explanation of the observations. (c) 2006 Elsevier B.V. All rights reserved.