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alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

bkit

compute_fep

Free energy perturbation for LAMMPS.

deeptime

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

ewald

intermol

Conversion tool for molecular simulations

mdtraj

An open library for the analysis of molecular dynamics trajectories

msm_we

History-augmented Markov analysis of weighted ensemble trajectories.

oeommtools

Tool collection to integrate and mix OpenEye and OpenMM

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openmm_orion

Cubes and Floes for running MD on the OpenEye Cloud Computing Platform Orion

parmed

Amber parameter topology file editor

pudl

The Public Utility Data Liberation Project provides analysis-ready energy system data to climate advocates, researchers, policymakers, and journalists.

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

synd

Library for easily creating and using highly efficient, arbitrarily complex synthetic dynamics models

westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

westpa2_tutorials

Tutorials and additional documentation for the WESTPA 2.0. (For future LiveCoMS Tutorial Paper)

westpa_tutorials

Tutorials and additional documentation for the WESTPA suite