A Practical Guide to DNA Origami Simulations Using NAMD
In this tutorial, we walk through the protocol for all-atom simulations of DNA origami using the NAMD package starting from a caDNAno design. As an example, we use a caDNAno design of a six-helix cylinder structure, which is provided in the tutorial archive. We will convert the caDNAno file to an all-atom structure file in the PDB format, solvate the all-atom structure in a MgCl2 solution, and perform MD simulations.