MCell Quick Reference Guide

Contents:

• 1. Running MCell3
• 2. Model Description Language overview
  • 2.1. The structure of an MDL file
  • 2.2. How to use this document
• 3. MDL commands
  • 3.1. Initialization commands
  • 3.2. Molecule definition commands
  • 3.3. Reaction definition commands
  • 3.4. Geometry definition commands
  • 3.5. Output specification commands
  • 3.6. Utility commands
• 4. Technical details affecting simulation speed and accuracy
  • 4.1. Partitioning
  • 4.2. Avoid Coincident Meshes
  • 4.3. Mean diffusion distance
  • 4.4. Reaction probabilities and Molecule Lifetimes
  • 4.5. Interaction radii
  • 4.6. Placing molecules in the world
• 5. Checkpointing Simulations
  • 5.1. Time Based Checkpointing
  • 5.2. Checkpointing with SIGUSR1 and SIGUSR2
• 6. Example models
  • 6.1. Ligand-gated ion channel
  • 6.2. Example bimolecular reaction
• 7. Authors

Indices and tables

• Index
• Search Page