Purpose Radiation-induced DNA damage arises from the direct action of generated ionizing particles on DNA constituent molecules and from indirect action mechanisms. Recent studies using Monte Carlo simulations with DNA models show that for 0.5 MeV to 10 MeV protons (within the energy range of interest in radiotherapy), most strand breaks (SBs) are due to indirect action. This study aims to quantify the risk of neutron-induced mutagenesis related to indirect action by determining neutron relative biological effectiveness (RBE) for clustered DNA damage as a function of neutron energy. Methods In a parallel study, the TOPAS-nBio framework was used to develop a nuclear DNA model, which we employ in this work to simulate the physical and chemical interactions between the products of water radiolysis and the DNA volumes. A comparison of generated G-values between TOPAS-nBio and Geant4-DNA was performed for validation. The chemical stage time resolution was adjusted to optimize speed without significant loss in G-value accuracy. Results The G-values of the two simulation frameworks were found to be consistent. The optimal time resolution was to logarithmically decrease the resolution as the chemical stage of the simulation progressed. Conclusions and Future Work A pipeline has been established to evaluate indirect DNA damage. An indirect clustered DNA damage scorer is currently under development to facilitate comparison between the indirect damage induced by secondary particles arising from a primary neutron spectrum and a reference radiation of 250 keV X-rays. Indirect SB yields will be compared with published data to validate our model.