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MDAnalysis is a Python library to analyze molecular dynamics trajectories.
Performance benchmarks of MDAnalysis provided by ASV.
Parallel algorithms for MDAnalysis
MDAnalysis home page mdanalysis.org as GitHub pages.
Notebooks for interactive use on https://mybinder.org/
MDAnalysis wrapper around Packmol
Python bindings for TNG file format
DocSearch - Configurations
Auto-generated docs for MDAnalysis
GridDataFormats provides the Python package 'gridData'. It contains a class ('Grid') to handle data on a regular grid --- basically NumPy n-dimensional arrays. It supports reading from and writing to some common formats (such as OpenDX).
A conda-smithy repository for mdanalysistests.
A conda-smithy repository for mdanalysis.
Numfocus Google Summer of Code Materials
Source code for HOLE program.
A conda-smithy repository for griddataformats.
A conda-smithy repository for mmtf-python.
Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
DSSP - Secondary structure analysis
Python bindings to STRIDE
STRIDE: Protein secondary structure assignment from atomic coordinates
Tutorial for MDAnalysis.
Tutorial for SPIDAL presentation at workshop, showing how to use Midas radical.pilot to analyze an ensemble of MD trajectories with Path Similarity Analysis (as implemented in MDAnalysis).
SciPy conference proceedings: MDAnalysis paper
A conda-smithy repository for rotamerconvolvemd.
Examples and tutorials of using MDAnalysis
Accepted proposal for a talk at SciPy 2016
port of C++ QuteMol
Python implementation of the fast rmsd and optimal rotation matrix method by Douglas Theobald and Pu Liu