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ionerdss (v.1.0) Documentation
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Creating NERDSS Inputs
----------------------

This section describes how to automatically create inputs for NERDSS.

.. toctree::
   :maxdepth: 1

   ionerdss_documentation_structure_of_nerdss_inputs
   ionerdss_documentation_from_pdb_structure
   ionerdss_documentation_from_platonic_solid
   ionerdss_gui
   java_gui
   gag_self_assembly_model

Analyzing NERDSS Outputs
------------------------

This section describes how to automatically analyze outputs for NERDSS.

.. toctree::
   :maxdepth: 1

   ionerdss_documentation_analyze_histogram
   ionerdss_documentation_transition_matrix
   ionerdss_documentation_location_analysis
   ionerdss_documentation_gag_self_assembly_analysis
   ionerdss_documentation_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.

.. toctree::
   :maxdepth: 1

   ionerdss_documentation_nerdss_gui