mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
lintf2_ether_ana_postproc
Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures
https://github.com/becksteinlab/propkatraj
pKa estimates for proteins using an ensemble approach
https://github.com/becksteinlab/imdclient
Streaming analysis from running MD simulations.
https://github.com/becksteinlab/mdanalysis-with-dask
Benchmarking MDAnalysis with dask.
rotamerconvolvemd
Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
https://github.com/bio-phys/pydiffusion
Analyse Rotational Diffusion Tensor from MD Simulations
https://github.com/becksteinlab/hop
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
https://github.com/bbye98/mdhelper
A batteries-included toolkit of analysis modules and helper functions for molecular dynamics (MD) simulations.
basicrta
Bayesian nonparametric inference of ligand binding kinetics from molecular dynamics simulations.
https://github.com/becksteinlab/parallel-analysis-in-the-mdanalysis-library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
mdtools
Scripts to prepare and analyze molecular dynamics simulations