Analysis of metadynamics simulations by metadynminer.py.

Abstract

Molecular dynamics simulation is very useful but computationally demanding method of studying dynamics of biomolecular systems. Many enhanced sampling methods were developed in order to obtain the desired results in available computational time. Metadynamics and its variants are common enhanced sampling methods used for this purpose. Metadynamics simulations allow the user to gather large amounts of data, which have to be analyzed to elucidate the properties of the studied system. Here, we present metadynminer.py, a Python package that allows easy and user-friendly analysis and visualization of the results obtained from metadynamics simulations. The built-in functions automate frequent tasks and make the package easy to use for new users, while its many customization options and object-oriented nature allow for integration into specialized data analysis workflows by more advanced users. The "metadynminer.py" Python package is available under the GPL-3.0 license via PyPi and Conda. The development version is available on GitHub along with issue support (https://github.com/Jan8be/metadynminer.py). Documentation, tutorial and Jupyter Notebook (provided through the public mybinder.org service) are available at https://metadynreporter.cz.