Welcome to CodeEntropy’s documentation!

This code is a complete and generally applicable set of tools for computing entropy of macromolecular systems from the forces sampled in a MD simulation.

Contents:

• Getting Started
  • Requirements
  • Installation
  • Input Files
  • Units
  • Quick Start
  • Working Directory and Output Location
  • Configuration and Arguments
  • Averaging
  • Counting Neighbours
  • Examples
  • Output Structure
• CodeEntropy
  • CodeEntropy package
• Multiscale Cell Correlation Theory
  • Key References
  • Additional application examples
  • Hierarchy
  • Vibrational Entropy
  • Conformational Entropy
  • Orientational Entropy
• Frequently asked questions
  • Why do I get a WARNING about invalid eigenvalues?
  • What do I do if there is an error from MDAnalysis not recognising the file type?
• Developer Guide
  • Getting Started for Developers
  • Running Tests
  • Regression Test Data
  • Coding Standards
  • Continuous Integration (CI)
  • Building Documentation
  • Contributing Code
  • Summary

Indices and tables

• Index

• Module Index

• Search Page