Conformational space of a porphyrin–fullerene dyad with the donor and acceptor connected by a relatively flexible linker is studied by molecular dynamics simulations in both non-polar and polar solvents, as well as in vacuum. The most probable conformations obtained from the vacuum MD simulations were optimized with semi-empirical (SE) and density functional theory (DFT) methods and the extent of the structural changes is assessed. The computational results indicate the co-existence of different conformers in both polar and nonpolar solvents showing agreement with experimental results. The most probable vacuum conformations at 300 K are similar to the ones at 0 K, while the structures most often observed in the solvents show less compact conformations. Optimization with SE and DFT calculations leads to structures, which represent relatively well the folded conformations in solvent, which validates the electronic structure calculations relevant to describing photoinduced electron-transfer in H2P–O34–C60.