Welcome to ThermoLIB!

ThermoLIB is a library developed at the Center for Molecular Modeling (CMM) for the application of Statistical Physics and/or Thermodynamics to molecular simulations. The library consists of two main sub modules:

• Thermodynamics - Module for reading, constructing, transforming and manipulating free energy profiles

• Kinetics - Module for computing the rate constant of a process/reaction using transition state theory (TST)

Citing ThermoLIB

If you used ThermoLIB in your research, please refer to ThermoLIB as follows:

13. Bocus, L. Vanduyfhuys, J. Chem. Inf. Model., 2026, 10.1021/acs.jcim.6c02199

This documentation contains instructions on how to install ThermoLIB, a user guide on all functionallities of the library as well as extensive tutorials illustrating the use of ThermoLIB in practice. Finally, there is also a reference guide included listing the call signatures of all available functions and classes. The documentation is structured as follows:

Table of Contents

• Installation Guide
  • Dependencies
  • Download and install ThermoLIB
  • Update ThermoLIB
  • Test installation
• User Guide
  • Constructing 1D histograms & free energy profiles
  • Constructing 2D histograms & free energy surfaces
  • Computing the correlation time
  • Error estimation
  • Plotting histograms and FEP/FES
  • Extracting micro- and macrostate free energy
  • Computing the reaction rate
  • Transformations of the FEP/FES
  • (De)projections of the FEP/FES
• Tutorials
  • Tutorial 1 - Construction of 1D free energy profile using WHAM
  • Tutorial 2 - Extracting kinetic reaction rates in 1D
  • Tutorial 3 - Construction of 2D free energy surface using WHAM
  • Tutorial 4 - Advanced techniques in error estimation
  • Tutorial 5 - Projection of 2D FES to 1D FEP with error propagation
  • Tutorial 6 - Deprojection to extract energetic contribution to free energy
  • Tutorial 7 - Transformations of 1D FEP and kinetics
  • Tutorial 8 - Transformation of 2D free energy surfaces
• Reference Guide
  • Thermodynamics – thermolib.thermodynamics
  • Kinetics – thermolib.kinetics
  • Error distributions – thermolib.error
  • Tools – thermolib.tools
  • Extensions – thermolib.ext

Support

For support and help you cannot extract from the guides and tuturials below, please contact us at louis.vanduyfhuys@ugent.be. It might be useful to check if the routine/class you are having troubles with has a verbose/verbosity keyword argument that you can use to give more logging output on what ThermoLIB is doing.