A Practical Guide to DNA Origami Simulations Using NAMD
Tutorial PDF: 
PDF icon origamiprotocols.pdf
Required tutorial files: 
Binary Data origamitutorial.tar.gz

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. 

Example applications

  • Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field
  • In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
  • De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation
  • Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating