ionerdss (v.1.0) Documentation

Creating NERDSS Inputs

This section describes how to automatically create inputs for NERDSS.

• Structure of the NERDSS Input Files
• Create NERDSS Input from PDB Structure
• Platonic Solid Self-assembly Input File Writing
• GUI to create .inp and .mol from user-defined molecules and reactions
• Creating Input Files with Java GUI
• Gag self assembly model

Analyzing NERDSS Outputs

This section describes how to automatically analyze outputs for NERDSS.

• Analyzing Histogram Files
• Analyzing Transition Matrix
• Locating position for certain size of complexes by PDB/restart file
• Sphere Regularization Index
• Merging results from restart simulations

Integrated GUI for NERDSS simulation and analysis

This section describes how to use the integrated GUI for NERDSS simulation and analysis.

• Integrated GUI for NERDSS simulation and analysis