# Index

# MCCE Documentation

## MCCE Documentation

#### What is MCCE?

- ##### [Multi-Conformation Continuum Electrostatics - MCCE](https://mccewiki.levich.net/books/what-is-mcce/page/multi-conformation-continuum-electrostatics-mcce)
- ##### [MCCE Mechanism](https://mccewiki.levich.net/books/what-is-mcce/page/mcce-mechanism)

#### [MCCE Success Stories](https://mccewiki.levich.net/shelves/mcce-success-stories)

- ##### [Proton Loading Sites in Complex I](https://mccewiki.levich.net/books/proton-loading-sites-in-complex-i/page/koreena-and-proton-loading-sites)
- ##### [MCCE Hydrogen Bond Characterization](https://mccewiki.levich.net/books/mcce-hydrogen-bond-characterization/page/gehan-and-mcce-microstates)
- ##### [Photosystem II Analysis](https://mccewiki.levich.net/books/photosystem-ii-analysis/page/jose-ortiz-soto-and-photosystem-ii)

#### [Quick Start](https://mccewiki.levich.net/shelves/quick-start)

- ##### [Install MCCE](https://mccewiki.levich.net/books/install-mcce/page/download-and-install-mcce)
- ##### [A simple MCCE example of pH titration](https://mccewiki.levich.net/books/a-simple-example/page/a-simple-mcce-example-of-ph-titration)

#### [Turtorials](https://mccewiki.levich.net/shelves/tutorials)

- ##### [Calculate pKas of Lysozyme - a 4-step process](https://mccewiki.levich.net/books/mcce-tutorial-4lzt/page/calculate-pkas-of-lysozyme-mcce-steps-1-4)
- ##### [Calculate Em of heme in Cytochrome](https://mccewiki.levich.net/books/calculate-em-of-heme-in-cytochrome/page/calculate-em-of-heme-in-cytochrome)
- ##### [Compute hydrogen bond network](https://mccewiki.levich.net/books/compute-hydrogen-bond-network/page/compute-hydrogen-bond-network)
- ##### [Sampling more rotamers at "hot" spots](https://mccewiki.levich.net/books/define-hot-spot-to-make-more-rotamers-in-mcce/page/sampling-more-rotamers-at-hot-spots)
- ##### [Gromacs Quick Start](https://mccewiki.levich.net/books/gromacs-quick-start)
    
    
    - ##### [Gromacs Server](https://mccewiki.levich.net/books/gromacs-quick-start/page/gromacs-server)
    - ##### [Example 1: Lysozyme](https://mccewiki.levich.net/books/gromacs-quick-start/page/example-1-lysozyme)
    - ##### [Example 2: Biphasic Systems](https://mccewiki.levich.net/books/gromacs-quick-start/page/example-2-biphasic-systems)
- ##### [Microstate Tools Tutorial](https://mccewiki.levich.net/books/microstate-tools-tutorial)
    
    
    - ##### [What is a microstate?](https://mccewiki.levich.net/books/microstate-tools-tutorial/page/what-is-a-microstate)
    - ##### [Tautomeric Charge Microstates](https://mccewiki.levich.net/books/microstate-tools-tutorial/page/tautomeric-charge-microstates)
- ##### [Run MCCE on Multiple PDBs at Once](https://mccewiki.levich.net/books/p-batch-tutorial/chapter/multiple-pdb-mcce-runs-pro-batch)

#### [Knowledgebase](https://mccewiki.levich.net/shelves/knowledgebase)

- ##### [MCCE Commands](https://mccewiki.levich.net/books/mcce-commands)
    
    
    - ##### [MCCE Program Run and Debug](https://mccewiki.levich.net/books/mcce-commands/page/mcce-program-run-and-debug)
    - ##### [MCCE Data Analysis](https://mccewiki.levich.net/books/mcce-commands/page/mcce-data-analysis)
    - ##### [MCCE Tools](https://mccewiki.levich.net/books/mcce-commands/page/mcce-tools)
- ##### [MCCE How Tos](https://mccewiki.levich.net/books/mcce-how-tos)
    
    
    - ##### [How to make a new topology file?](https://mccewiki.levich.net/books/mcce-how-tos/page/how-to-make-a-new-topology-file)
    - ##### [How to add rotamer making rules to parameter file?](https://mccewiki.levich.net/books/mcce-how-tos/page/how-to-add-rotamer-making-rules-to-parameter-file)
- ##### [Other HOW-TOs](https://mccewiki.levich.net/books/other-how-tos)
    
    
    - ##### [How to install WSL (Windows Subsystem Linux)](https://mccewiki.levich.net/books/other-how-tos/page/how-to-install-wsl-windows-subsystem-linux)
    - ##### [How to contribute code to MCCE](https://mccewiki.levich.net/books/other-how-tos/page/how-to-contribute-code-to-mcce)
- ##### [Microstate Analysis Library](https://mccewiki.levich.net/books/microstate-analysis-library)
    
    
    - ##### [Microstate Analysis Library Reference](https://mccewiki.levich.net/books/microstate-analysis-library/page/microstate-analysis-library-reference)
- ##### [Interprete MCCE Results](https://mccewiki.levich.net/books/results)
    
    
    - ##### [How does changing MCCE's parameters change accuracy?](https://mccewiki.levich.net/books/results/page/how-does-changing-mcces-parameters-change-accuracy-under-construction)
    - ##### [How to break down the energy of a residue ionization?](https://mccewiki.levich.net/books/results/page/how-to-break-down-the-energy-of-a-residue-ionization)