@MDAnalysis
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MDAnalysis

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Top repositories

1

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
Python
1,277
star
2

WorkshopMDMLEdinburgh2022

Jupyter Notebook
63
star
3

solvation-analysis

A comprehensive tool for analyzing liquid solvation structure.
Python
45
star
4

MDAnalysisCookbook

Examples and tutorials of using MDAnalysis
41
star
5

pmda

Parallel algorithms for MDAnalysis
Python
31
star
6

WorkshopPrace2021

Materials for the 2021 PRACE Workshop @ SurfSARA
Jupyter Notebook
31
star
7

panedr

Reads Gromacs EDR file to populate a pandas dataframe
Python
30
star
8

membrane-curvature

MDAnalysis tool to calculate membrane curvature.
Python
29
star
9

GridDataFormats

GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.
Python
29
star
10

MDAPackmol

MDAnalysis wrapper around Packmol
Python
25
star
11

UserGuide

User Guide for MDAnalysis
Python
22
star
12

mdacli

Command line interface for MDAnalysis
Python
19
star
13

MDAKits

The MDAnalysis Toolkits Registry
Python
15
star
14

MDAnalysis.github.io

MDAnalysis home page mdanalysis.org as GitHub pages.
CSS
14
star
15

MDAnalysisData

Access to data for workshops and extended tests of MDAnalysis.
Python
14
star
16

WorkshopHackathon2018

Materials, issues and things for the 2018 Workshop and Hackathon
Jupyter Notebook
14
star
17

pytng

Python bindings for TNG file format
C
13
star
18

MDAnalysisMolSSIWorkshop-Intermediate2Day

Jupyter Notebook
12
star
19

MDAnalysisTutorial

Tutorial for MDAnalysis.
Jupyter Notebook
11
star
20

distopia

SIMD instructions for faster distance calculations.
C++
10
star
21

stride

STRIDE: Protein secondary structure assignment from atomic coordinates
C
10
star
22

transport-analysis

A Python package to compute and analyze transport properties.
Python
9
star
23

cookiecutter-mdakit

Cookiecutter for Python packages based on MDAnalysis
Python
7
star
24

cellgrid

Python
7
star
25

RotamerConvolveMD

Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
Python
7
star
26

MDAnalysisWorkshop-Intro0.5Day

Materials for 0.5-day MDAnalysis workshops
Jupyter Notebook
6
star
27

waterdynamics

Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
Python
5
star
28

mdahole2

An MDAKit implementing a Python interface for the HOLE program.
Python
5
star
29

pystride

Python bindings to STRIDE
Python
4
star
30

UGM2023

Materials for the 2023 MDAnalysis User Group Meeting
Jupyter Notebook
4
star
31

mdalint

Proof of concept for a MDAnalysis linter
Python
4
star
32

binder-notebook

Notebooks for interactive use on https://mybinder.org/
Jupyter Notebook
4
star
33

dssp

DSSP - Secondary structure analysis
C++
3
star
34

pyQuteMol

port of C++ QuteMol
Python
3
star
35

RDKitConverter-benchmark

Benchmark for the RDKitConverter's inferring of bond orders and charges
HTML
3
star
36

scipy-2016

Accepted proposal for a talk at SciPy 2016
TeX
2
star
37

mdakits-whitepaper

MDAKits whitepaper (LaTeX sources).
TeX
2
star
38

MDAnalysisSandbox

testing reporsitory for workshops
Python
2
star
39

benchmarks

Performance benchmarks of MDAnalysis provided by ASV.
Shell
2
star
40

MDAnalysisWorkshop-Intro1Day

Materials for 1-day MDAnalysis workshops
Jupyter Notebook
2
star
41

SPIDAL-MDAnalysis-Midas-tutorial

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).
Python
1
star
42

.github

MDAnalysis Org profile
1
star
43

mdanalysis-sphinx-theme

The official MDAnalysis Sphinx documentation theme.
Sass
1
star
44

mdgeomkit

Simple cookie-cutter based MDAKit (for Workshop teaching)
Python
1
star
45

UGM2024

Materials for the 2024 MDAnalysis User Group Meeting
1
star
46

binder-env-userguide

Binder environment of the User Guide
1
star
47

mdanalysis-compatible-python

Python
1
star
48

mda-xdrlib

Stand-alone XDRLIB module (from cpython 3.10.8)
Python
1
star
49

get-latest-python-version

Python
1
star