Molecular dynamics data for DNA base flipping

DNA base flipping trajectory files. Initial state is a double stranded DNA containing a thymine mutated to a uracil. Uracil is then flipped out according to a 100ns simulation. The DNA structure was created with the w3DNA tool, with a uracil replacing thymine in position 12. The structure was solvated with tip3p water model and 0.15 mol sodium and chloride added to neutralize the system. Minimization, equilibration and production were performed on the system to obtain a stable configuration. Then a metadynamic simulation was run for uracil base flipping using the NAMD tool, with charmm36 force field. The 'input' folder contains the input files to run the simulation. The 'output' folder contains the trajectory.