Multi-resolution DNA nanostructures

This tutorial introduces a Python3 package called mrdna that makes it easy to run simulations of DNA nanotechnology objects. The multi-resolution approach provides the benefits of coarse-grained modeling, while resulting in a high-resolution structure suitable for atomistic simulations.

Getting started

Required hardware and operating system

Please note that this tutorial is written for the linux platform and x86 architecture. Proceed at your own risk using other operating systems and architectures. Currently, a CUDA-enabled GPU is required for running simulations using the ARBD engine.

Required software

Make sure you have the mrdna package properly installed. You will also need the jupyter package installed to your Python environment. Finally, you will need to install VMD, NAMD and ARBD.

Instructions

Follow the pdf for steps 1-2, which cover the usage of a command line utility that makes fast multi-resolution simulations of DNA objects very easy to perform. Then launch the Jupyter notebook "step3.ipynb" for an introduction to scripting with the mrdna framework. If you have any questions or concerns, please contact Chris Maffeo at cmaffeo2@illinois.edu.