This paper presents an optimized protocol for in vacuo molecular dynamics studies of short DNAduplexes containing modified nucleosides. The example studied is an 11 base pair DNA duplex modifiedwith l,N6-ethenodeoxyadenosine (dεA) located opposite deoxyguanosine. A complex moleculardynamics trajectory was subjected to statistical cluster analysis. Groups (clusters) of similarconformations, which can be statistically identified after energy minimization of the trajectory results,have been analyzed with particular regard to the estimation of intrinsic stability of the duplex (hydrogenbonding and base stacking). The modified residue was found to form two hydrogen bonds within thed ε A / d G base pair, which stabilize the duplex, thus allowing its conformation to remain close to regularB-DNA.