DoMD

Manual:

  • Preface and Disclaimer
  • Introduction
  • Installation Guide
  • Running the Examples
  • Component of Code
  • Wrapped functions
  • Input Configuration and File Format
  • S-CGFG Algorithm
  • Force Field Assignment
  • Custom Force Field Construction

Tutorials:

  • Linear Polymer (examples/pi)
  • Brush Polymer (examples/spes_brush)
  • Crosslinked Networks (examples/spes_network)
  • Lipid Membranes & Protein-Loaded NPs (examples/aunps)
  • Core-Shell Nanoparticles (examples/core_shell_nps)

API Reference:

  • domd_cgbuilder package
  • domd_database package
  • domd_forcefield package
  • domd_topology package
  • domd_xyz package
    • Subpackages
      • domd_xyz.embed package
    • Submodules
    • domd_xyz.embed_molecule module
    • Module contents
  • misc package
DoMD
  • domd_xyz package
  • View page source

domd_xyz package

Subpackages

  • domd_xyz.embed package
    • Submodules
    • domd_xyz.embed.embed_with_cg_xyz module
    • domd_xyz.embed.optimize_orientation module
    • Module contents

Submodules

domd_xyz.embed_molecule module

Module contents

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© Copyright 2026, Ming-yang Li, Rui Shi, Hu-jun Qian (hjqian@jlu.edu.cn).

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