oxDNA setup for mrDNA simulations

[FionaSander]

The idea is to set up a script which generates a file containing a defined system of dsDNA and ssDNA. The length, percentage etc. of both components will be varied in order to find the optimum system.

• [x] create a long strand of DNA that has single-stranded portions, and double-stranded portions
• [x] 200-300 bases in a per piece of DNA
• [ ] 100s of these
• parameters:
  • [x] length of the whole piece
  • [ ] % of double-stranded vs. single-stranded
  • [ ] patterns