What is 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:

• Thermodynamics - Module for constructing, manipulating and post-processing of 1D free energy profiles (FEP) and 2D free energy surfaces (FES). Functions include

  • construction of FEPs using WHAM including error estimatoin
  • definition of (meta)stable micro- and macrostates
  • transformation of FEPs from one collective variable to another
  • (de)projection of a FES to a lower/higher dimensional FES.

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

  • compute rate constant (which is theoretically indepedent of used CV)
  • compute associated phenomenological free energy barrier
  • error propagation from FEP to rate constant/phenomenological barrier

Documentation

More information on how to use ThermoLIB, including tutorials, can be found in its manual at https://molmod.github.io/ThermoLIB/.

How to cite ThermoLIB

If you use ThermoLIB in your research, please cite it as follows:

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

How to install?

ThermoLIB has the following dependencies:

• Cython
• numpy
• scipy
• scikit-learn
• matplotlib
• h5py
• ase (Version 3.23.0 or newer)

To install ThermoLIB using pip either download the master branch as zip, go to your desired pip environment and run

pip install ThermoLIB-master.zip

or if you have set up your ssh config file to access github.com using key authentication through an alias defined as 'github', you can install ThermoLIB as follows:, you can simply run:

pip install git+ssh://github/molmod/ThermoLIB.git

Terms of use

ThermoLIB is mainly developed by prof. Louis Vanduyfhuys at the Center for Molecular Modeling. Usage of ThermoLIB should be requested with prof. Vanduyfhuys.

Copyright (C) 2019 - 2026 Louis Vanduyfhuys Louis.Vanduyfhuys@UGent.be Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise stated.