This repository contains the data and analysis presented in the article entitled "Proton Transfer During DNA Strand Separation as a Source of Mutagenic Guanine-Cytosine Tautomers".
The following files can be used to reproduce molecular dynamics files in Gromacs 2018 with the CHARMM36 and SPCE force fields:
- DNA14_rdy.gro (Solvated and neutralised double stranded DNA with 14 basepairs)
- min.mdp (minimisation control file)
- eq500ps_dna.mdp (equilibration NVT control file)
- md200ps_dna_pull90min.mdp (example SMD control file)
- long paths, paths longer than 2A separation distance
- paths, 0-9 ordered in increasing separation distance according to manuscript
- stacked, calculations on reaction path including stacking interactions