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MCell Quick Reference Guide 3.2.1 documentation
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MCell Quick Reference Guide
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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
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