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:
Table of Contents
- Installation Guide
- 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
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.