  A polarizable environment, prominently the solvent, responds to electronic
changes in biomolecules rapidly. The knowledge of conformational relaxation of
the biomolecule itself, however, may be scarce or missing. In this work, we
describe in detail the structural changes in DNA undergoing electron transfer
between two adjacent nucleobases. We employ an approach based on averaging of
tens to hundreds of thousands of nonequilibrium trajectories generated with
molecular dynamics simulation, and a reduction of dimensionality suitable for
DNA. We show that the conformational response of the DNA proceeds along a
single collective coordinate that represents the relative orientation of two
consecutive base pairs, namely, a combination of helical parameters shift and
tilt. The structure of DNA relaxes on time scales reaching nanoseconds,
contributing marginally to the relaxation of energies, which is dominated by
the modes of motion of the aqueous solvent. The concept of reaction path
averaging (RPA), conveniently exploited in this context, makes it possible to
filter out any undesirable noise from the nonequilibrium data, and is
applicable to any chemical process in general.
