apallath / postmetad

Python package for post-processing PLUMED metadynamics and OPES simulations.

postmetad

postmetad is a Python package for post-processing PLUMED Metadynamics and On-the-fly Probability Enhanced Sampling (OPES) simulations.

postmetad.metad can reconstruct biases and free energy profiles from METAD output files, while postmetad.opes_metad can reconstruct biases and free energy profiles from OPES_METAD output files.

Installation

Clone the sources with git, and run

pip install [-e] .

at the top level directory of the repository.

Usage

Read the documentation at apallath.github.io/postmetad

References

1. Laio, A., & Parrinello, M. (2002). Escaping free-energy minima. Proceedings of the National Academy of Sciences, 99(20), 12562–12566. DOI
2. Invernizzi, M., & Parrinello, M. (2020). Rethinking metadynamics: From bias potentials to probability distributions. The Journal of Physical Chemistry Letters, 11(7), 2731–2736. DOI