MDAKits and MDA-based tools
MDAnalysis is developed with extensibility in mind, allowing
scientists to create various tools with the components
that the library provides. To help developers in this process,
and to advertise these wonderful tools to the MDAnalysis user community,
we have created an ecosystem of MDAnalysis Toolkits, or “MDAKits”.
MDAKits
Please look at the registry of MDAKits
for a list of toolkits that meet the minimum MDAKit requirements.
These are regularly tested against the latest and development versions of
MDAnalysis. Whilst we cannot guarantee the completeness of the MDAKit’s test coverage, if you see a green badge, the code should be minimally behaving as the MDAKit authors intended it!
If you have your own MDAKit and you would like to add it to the
registry, please look at the contribution instructions
or share it on GitHub Discussions!
Below we list projects that use MDAnalysis and are not registered as MDAKits:
-
nglview: nglview is a tool to visualize
trajectories in jupyter notebooks.
-
MDSrv streams and visualizes MD trajectories interactively within web browsers
-
MD Trajectories in
PyMOL: MDAnalysis has
been embedded into Open Source PyMOL to read many different MD formats
directly. Source code is available from
bieniekmateusz/pymol-mdanalysis on GitHub.
-
MolecularNodes plugin for the Blender rendering package; the plugin provides a convenient method for importing structural biology files, including MD trajectories, into Blender, and several nodes for working with atomic data inside of Blender’s Geometry Nodes.
-
pydiffusion: Analyze the
rotational diffusion of your molecules.
-
pytim: Pytim is a package based on
MDAnalysis for the identification and analysis of surface molecules in
configuration files or in trajectories from molecular dynamics simulations.
-
pycontact: Analysis of
non-covalent interactions in MD trajectories.
-
RotamerConvolveMD:
Analysis of molecular dynamics trajectories or conformational ensembles in
terms of spin-label distances as probed in double electron-electron resonance
(DEER) experiments.
-
PBxplore: PBxplore is a suite of
tools dedicated to Protein Block (PB) analysis.
-
cgheliparm: Scripts used to analyze
dsDNA structures from Martini MD simulations.
-
accelerated_sampling_with_autoencoder:
This is the framework for running accelerated sampling with data-augmented
autoencoders.
-
BioEn: BioEn integrates a broad range of experimental data to refine ensembles of structures.
-
kugupu: A molecular network generator to study charge transport pathways in amorphous materials
-
PyInteraph: A software tool
for the analysis of structural communication in protein ensembles,
including a PyMOL plugin and an InteractionPlotter.
-
MAICoS: Analyze molecular dynamics simulations of
interfacial and confined systems.
-
taurenmd: A command-line interface for analysis of Molecular Dynamics simulations.
-
PENSA: A toolkit for exploratory analysis and comparison of protein structural ensembles
-
LiPyphilic: A Python package for the analysis of lipid membrane simulations.
-
MDVoxelSegmentation: A voxel-based approach for dynamic cluster analysis of molecular dynamics trajectories.
-
Swarm-CG: Automatically optimizes the bonded terms of a MARTINI-like coarse-grained (CG) molecular model with respect to its reference all-atom (AA) trajectory, via FST-PSO.
Simulation packages
-
ESPResSo is a software package for
performing and analyzing Molecular Dynamics many-particle
simulations of coarse-grained atomistic or bead-spring models as
they are used in soft matter research in physics, chemistry and
molecular biology.
Distributions
MDAnalysis is included in NMRBox a distribution of
common software to analyze NMR measurements.
Some generic distributions such as MacPorts:
py-MDAnalysis
(macOS), Fedora:
python-MDAnalysis
and archlinux:
python-mdanalysis
(Linux) maintain packages of MDAnalysis.