GitHub topics: mdanalysis
MDAnalysis/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Language: Python - Size: 511 MB - Last synced at: about 7 hours ago - Pushed at: 4 days ago - Stars: 1,423 - Forks: 711
chemosim-lab/ProLIF
Interaction Fingerprints for protein-ligand complexes and more
Language: Python - Size: 11.3 MB - Last synced at: about 10 hours ago - Pushed at: about 11 hours ago - Stars: 410 - Forks: 80
MDAnalysis/benchmarks
Performance benchmarks of MDAnalysis provided by ASV.
Language: Shell - Size: 597 MB - Last synced at: about 11 hours ago - Pushed at: 3 days ago - Stars: 2 - Forks: 1
NMRDfromMD/dataset-LJ-fluid
This repository contains a dataset for the NMRDfromMD Python package.
Language: Jupyter Notebook - Size: 57 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0
NMRDfromMD/nmrdfrommd.github.io
This repository contains the documentation for the NMRDfromMD Python package.
Size: 31.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 0
NMRDfromMD/dataset-peg-water-mixture
This repository contains a dataset for the NMRDfromMD Python package.
Language: Python - Size: 7.81 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0
calpolyccg/MDSAPT
SAPT energy calculator built using MDAnalysis and Psi4
Language: Python - Size: 8.49 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 14 - Forks: 5
chenggroup/ai2-kit
A toolkit featured artificial intelligence × ab initio for computational chemistry research.
Language: Python - Size: 8.31 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 62 - Forks: 13
MDAnalysis/membrane-curvature
MDAnalysis tool to calculate membrane curvature.
Language: Python - Size: 42.3 MB - Last synced at: 5 days ago - Pushed at: 9 months ago - Stars: 32 - Forks: 8
MDAnalysis/mdahole2
An MDAKit implementing a Python interface for the HOLE program.
Language: Python - Size: 15.3 MB - Last synced at: about 12 hours ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 3
BioMemPhys-FAU/domhmm
Open source package to identify nano- and microdomains in Molecular Dynamics simulations of bio-membranes.
Language: Python - Size: 68 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
Becksteinlab/imdclient
Streaming analysis from running MD simulations.
Language: Python - Size: 374 MB - Last synced at: 29 days ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 0
MDAnalysis/MDAnalysisData
Access to data for workshops and extended tests of MDAnalysis.
Language: Python - Size: 7.12 MB - Last synced at: 5 days ago - Pushed at: 8 months ago - Stars: 17 - Forks: 4
Becksteinlab/propkatraj
pKa estimates for proteins using an ensemble approach
Language: Python - Size: 9.32 MB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 28 - Forks: 6
yuxuanzhuang/ggmolvis
Molecular visualization for MDAnalysis with MolecularNodes in Blender
Language: Python - Size: 81.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 16 - Forks: 3
MDAnalysis/WorkshopPrace2021
Materials for the 2021 PRACE Workshop @ SurfSARA
Language: Jupyter Notebook - Size: 34.8 MB - Last synced at: 5 days ago - Pushed at: over 3 years ago - Stars: 30 - Forks: 5
Marcello-Sega/pytim
a python package for the interfacial analysis of molecular simulations
Language: Python - Size: 206 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 85 - Forks: 35
MDAnalysis/imd-workshop-2024
Materials for the virtual 2024 MDAnalysis IMD streaming workshop.
Language: Jupyter Notebook - Size: 25.5 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 7 - Forks: 1
Becksteinlab/zarrtraj
zarrtraj MDAKit for @MDAnalysis
Language: Jupyter Notebook - Size: 26.8 MB - Last synced at: 22 days ago - Pushed at: 3 months ago - Stars: 8 - Forks: 2
andthum/lintf2_ether_ana_postproc
Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures
Language: Python - Size: 1.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
andthum/transfer_Li
Transfer Li ions from cathode to anode in MD simulations
Language: Shell - Size: 200 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
andthum/mdtools
Scripts to prepare and analyze molecular dynamics simulations
Language: Python - Size: 12.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 2
Becksteinlab/basicrta
Bayesian nonparametric inference of ligand binding kinetics from molecular dynamics simulations.
Language: Python - Size: 10.6 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 0 - Forks: 3
ravenswing/mdsaps
Molecular Dynamics - Simulation Analysis and Preparation Suite
Language: Python - Size: 1020 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0
MDAnalysis/mdacli
Command line interface for MDAnalysis
Language: Python - Size: 7.15 MB - Last synced at: 5 days ago - Pushed at: 10 months ago - Stars: 20 - Forks: 7
2253shubham/2PT-for-isotherms
Two Phase Thermodynamic (2PT) Method to compute adsorption isotherms
Language: Python - Size: 89.8 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
simongravelle/MDAnalysis-tutorial
Perform post-mortem analysis using Python and MDAnalysis
Language: Jupyter Notebook - Size: 25.7 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 5 - Forks: 0
MDAnalysis/pmda
Parallel algorithms for MDAnalysis
Language: Python - Size: 6.71 MB - Last synced at: 5 days ago - Pushed at: 9 months ago - Stars: 31 - Forks: 23
Becksteinlab/Parallel-analysis-in-the-MDAnalysis-Library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
Language: Python - Size: 78.1 KB - Last synced at: 20 days ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 4
paulshamrat/ColabMDA
User friendly molecular dynamics simulation combining GROMACS and Google Colab: A complete guide
Language: Jupyter Notebook - Size: 112 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 8 - Forks: 3
AngelRuizMoreno/Jupyter_Dock
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
Language: Jupyter Notebook - Size: 30.8 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 260 - Forks: 67
bio-phys/pydiffusion
Analyse Rotational Diffusion Tensor from MD Simulations
Language: Jupyter Notebook - Size: 564 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 17 - Forks: 4
Becksteinlab/imdreader 📦
prototype IMDReader for MDAnalysis
Language: Python - Size: 6.91 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0
Becksteinlab/hop
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
Language: Python - Size: 16.9 MB - Last synced at: 20 days ago - Pushed at: over 6 years ago - Stars: 14 - Forks: 5
ravenswing/phd_tools
Auxiliary tools and scripts initially made for my PhD projects.
Language: Jupyter Notebook - Size: 167 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
usuaero/MachUpX
Fast and accurate aerodynamic modeling using general numerical lifting-line theory.
Language: Python - Size: 16.7 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 86 - Forks: 15
bbye98/mdhelper 📦
A batteries-included toolkit of analysis modules and helper functions for molecular dynamics (MD) simulations.
Language: Python - Size: 87.8 MB - Last synced at: 8 days ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0
MDAnalysis/RotamerConvolveMD
Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
Language: Python - Size: 9.12 MB - Last synced at: 5 days ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 4
MolSSI/mmic_mda
Tactic MMIC translator for MDAnalysis/MMSchema
Language: Python - Size: 3.74 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 2
theavey/ParaTemp
A package for molecular dynamics analysis and parallel tempering in GROMACS
Language: Python - Size: 1.19 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 11 - Forks: 4
alec-glisman/Analysis-Two-Chain-PAA
Analyze interactions between two fully-charged PAA chains with varying amounts of CaCl2 added
Language: Python - Size: 22.5 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
cschmidtlab/syt1_membrane_md
Python code for publication investigating Synaptotagmin-1 membrane interaction
Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
wesbarnett/libxdrfile 📦
Fork of library used in reading xtc files from GROMACS simulations
Language: C - Size: 53.7 KB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 12 - Forks: 12
seunginhwang/MD-anaysis-code
About This is code for analyzing the xtc file used in GROMACS, a molecular dynamics simulation program.
Language: Python - Size: 4.88 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
sbrodehl/MD-AlanineDipeptide
Molecular Dynamics Simulation of Alanine Dipeptide and Dihedral Angle Analysis
Language: Python - Size: 3.6 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 0
Moutoussamy/HelixAngle
Python module: Calculation of helices angle during MD
Language: Python - Size: 603 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0
urastogi885/classify-it
Face recognition using various classifiers
Language: MATLAB - Size: 11.1 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
siddharthtelang/Face-and-Pose-Classification
Face detection (class and pose) using various Classifiers - Own Implementation
Language: Jupyter Notebook - Size: 17.9 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
Becksteinlab/MDAnalysis-with-Dask
Benchmarking MDAnalysis with dask.
Language: Python - Size: 1.15 MB - Last synced at: 20 days ago - Pushed at: over 7 years ago - Stars: 5 - Forks: 1
kain88-de/mdacli
some simple CLI tools written with MDAnalysis.
Language: Python - Size: 19.5 KB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0
jeiros/Scripts
Compilation of different scripts used for my MD analysis
Language: Python - Size: 2.01 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 2
RayLabIIITD/pyLFDA
pyLFDA is a tool which allows analysis of pairwise lipid force distribution along with other functions such as curvature and diffusion.
Language: Jupyter Notebook - Size: 88.6 MB - Last synced at: 29 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0
datreant/MDSynthesis
a logistics and persistence engine for the analysis of molecular dynamics trajectories
Language: Python - Size: 14.1 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 30 - Forks: 6
PicoCentauri/mdacli Fork of MDAnalysis/mdacli
Command line interface for MDAnalysis
Language: Python - Size: 6.66 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
aakognole/drude_prepper_analysis
Analysis scripts for the CHARMM GUI Drude Prepper Paper
Language: Rich Text Format - Size: 30.9 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1
MDAnalysis/mdakits-whitepaper
MDAKits whitepaper (LaTeX sources).
Language: TeX - Size: 411 KB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
ojeda-e/cookiecutter-analysis Fork of MolSSI/cookiecutter-cms
Cookiecutter repo for MD analysiS -standalone-.
Size: 269 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
MDAnalysis/binder-notebook
Notebooks for interactive use on https://mybinder.org/
Language: Jupyter Notebook - Size: 821 KB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 8
MDAnalysis/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).
Language: Python - Size: 3.47 MB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 2
born-2learn/molecular-dynamics-sasa
FreeSASA and MDAnalysis trials
Language: Python - Size: 65.4 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
