Project files provided as supporting information to the manuscript: "Dynamical insights on the role of supercoiling on DNA radiosensitivity"

README file to the Zenodo repository provided as supporting information to the manuscript.Authors: Manuel Micheloni, Raffaello Potestio, Lorenzo Petrolli ============================================== The archive 00_ShootingInTimeWindows.tar.gz contains the MD simulations of a 672-bp DNA minicircle with a single DSB introduced either in the loop or in the supercoiled region.Each MD replicate has been carried out in three steps: (1) relaxation with a Bussi thermostat, (2) thermalization with a Langevin thermostat, and (3) a production run of the damaged DNA. We employed the oxDNA2 force field, with both a sequence-averaged (SequenceAvg_Interaction) and seqeunce-dependent (SequenceDep_Interaction) parametrization. Example scripts can be found in SIM/MD_scripts. Each "DSB#" folder corresponds to one of three supercoiling levels, namely sigma = 0, -0.06, +0.06. Within these folders, time intervals (TW#) are organized into two subfolders: “data” and “input_structure”. The “data” folder includes the pair-wise energy contributions at the lesion interface (subfolder “1.E”), while the snapshots of the systems at the end of steps (2) (containing "_Relax2_") and (3) are reported in subfolder “2.traj”.The “input_structure” folder contains the .top and .dat oxDNA files of the damaged DNA. Lesions are enforced on the minicircles at the end of stage (2). The extended MD replicates used to compute the free energy landscapes, as well as the analysis of the superhelical density relaxation (i.e., Figures S1, S2, S3, S4, S5), whose composite compressed size is about 80 GB, are available upon request.