  We consider an open molecular junction in which electrons are coupled to
multi-mode phonons. Using a master equation approach for equilibrated phonons,
we show that nearly-degenerate phonon modes can be mapped into an effective
single mode, which can result in a noticeable reduction of computational costs.
As an illustration, we apply our theory to the OPV-5 molecule and show that we
can obtain the consistent conductance spectra while reducing the computational
time by orders of magnitude
