ENPMDA 0.3.0

parallel analysis for ensemble simulations

Ensemble Parallel MDAnalysis

Warning

This is still under constrution.

ENPMDA

Parallel analysis for ensemble simulations powered by MDAnalysis. ENPMDA stores metadata in pandas.DataFrame and distributes computation jobs in dask.DataFrame so that the parallel analysis can be performed not only for one single trajectory but also across simulations and analyses.

It can be used as an initial inspection of the raw trajectories as well as a framework for extracting features from final production simulations for further e.g. machine learning and markov state modeling. It automatically fixes the PBC issue and align and center the protein inside the simulation box. It also works for multimeric proteins!

The framework is intended to be adaptable by being able to simply wrapping MDAnalysis analysis functions without worrying about the parallel machinery behind.

• Free software: GNU General Public License v3

• Documentation: https://ENPMDA.readthedocs.io.

Features

• Parallel analysis for ensemble simulations.

• Dataframe for storing and accessing results.

• dask-based task scheduler, suitable for both workstations and clusters.

• Expandable analysis library powered by MDAnalysis.

Workflow Illustration

TODO

• more analysis functions.

• unit testing

• benchmarking

• option to retrieve numerical results

• documentation

• add functions to cancel running tasks

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.0 (2022-05-09)

• First release on PyPI.