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ionerdss 1.1.0 documentation
ionerdss 1.1.0 documentation
  • Installation Guide
  • Release Notes
  • NERDSS Documentation
    • NERDSS User Guide
      • Dependencies
      • Building NERDSS
      • Starting a Simulation With NERDSS
      • Running a Restart Simulation
      • Restarting and Modifying the System
      • Input and Output Files of NERDSS
      • Important Considerations for Reaction Rates
      • NERDSS and Time-Step Selection
      • Creating Input Files With JAVA GUI
      • References
    • NERDSS Developer Guide
      • Key Data Structures
      • Volume Exclusion Implementation
      • Enforcement of Reaction and Diffusion Events per Timestep (Δt)
      • Handling High Reaction Probabilities
      • Syntax and Formatting
      • Adding Input Parameters
      • Adding a New Reaction Type
      • Debugging
      • Compiling
      • Profiling
    • NERDSS parallel Developer Guide
      • Serial NERDSS
      • Parallel NERDSS
      • Debugging
  • ionerdss (v.1.0) Documentation
    • 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 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
  • Tutorials
    • 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
  • API Reference
    • ionerdss
      • ionerdss package
        • ionerdss.nerdss_simulation package
        • ionerdss.nerdss_analysis package
        • ionerdss.model_setup package
          • ionerdss.model_setup.database_pdb package
            • ionerdss.model_setup.database_pdb.gen package
          • ionerdss.model_setup.gag_reshape package
            • ionerdss.model_setup.gag_reshape.sphere_reg package
          • ionerdss.model_setup.nerdss_gui package
            • ionerdss.model_setup.nerdss_gui.gen package
          • ionerdss.model_setup.platonic_solids package
            • ionerdss.model_setup.platonic_solids.cube package
            • ionerdss.model_setup.platonic_solids.dode package
            • ionerdss.model_setup.platonic_solids.gen_platonic package
            • ionerdss.model_setup.platonic_solids.icos package
            • ionerdss.model_setup.platonic_solids.octa package
            • ionerdss.model_setup.platonic_solids.tetr package
        • ionerdss.analysis package
          • ionerdss.analysis.acf package
          • ionerdss.analysis.file_managment package
          • ionerdss.analysis.histogram package
            • ionerdss.analysis.histogram.multi_species package
            • ionerdss.analysis.histogram.single_species package
          • ionerdss.analysis.locate_pos package
            • ionerdss.analysis.locate_pos.nerdss_PDB package
            • ionerdss.analysis.locate_pos.restart package
          • ionerdss.analysis.transition_matrix package
          • ionerdss.analysis.xyz package
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NERDSS Documentation¶

Non-Equilibrium Reaction Diffusion Self-Assembly Simulator

  • NERDSS User Guide
  • NERDSS Developer Guide
  • NERDSS parallel Developer Guide
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