Tutorials

The tutorials for ioNERDSS are provided as Jupyter notebooks, demonstrating how to:

• Set up models for NERDSS

• Read and process simulation outputs

• Generate plots and analyses

Notebook Index

For detailed description of NERDSS inputs and outputs, please refer to the NERDSS User Guide.

Below is a quick reference for the available Jupyter notebooks to prepare the input files and analyze the output files of NERDSS simulations:

Jupyter Notebooks

• Quick Start Demo (ionerdss v.1.1.0)
• PDB to NERDSS Converter Tutorial
• Setup Self-assembly Model for Platonic Solid (Dodecahedron as Example)
• Tutorial for Reading Structures from Protein Data Bank (PDB) Files and Generating Inputs for NERDSS
• ioNERDSS Python Package Tutorial for Single-species Assembly
• ioNERDSS Python Package Tutorial for Multi-species Assembly
• Graphic User Interface (GUI) Tutorial
• Tutorial for Clathrin Self-assembly Simulation
• Tutorial for GagSphere Simulation

Additional Resources

• For function-by-function details, see the API Reference.

• For installation instructions, see the Installation Guide.