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GromacsWrapper
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).propkatraj
pKa estimates for proteins using an ensemble approachMDPOW
Calculation of water/solvent partition coefficients with Gromacs.PSAnalysisTutorial
Examples and data for performing path similarity analysis (PSA).hop
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.making-prettier-plots
a quick primer on making prettier (and more impactful) plotsMDAnalysis-workshop
MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshopAdKGromacsTutorial
Basic tutorial for running and analyzing a Gromacs MD simulation of AdKmdworks
molecular dynamics, with Fireworks!vesicle_library
library of vesicles with the Dry Martini force fieldhollow
Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).MDAnalysis-with-Dask
Benchmarking MDAnalysis with dask.zarrtraj
zarrtraj MDAKit for @MDAnalysismultibind
A Python package for building thermodynamically consistent state graphs.kda
Python package used for the analysis of biochemical kinetic diagrams.Parallel-analysis-in-the-MDAnalysis-Library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.numkit
Numerical first aid kit (with numpy/scipy).workflows-talk
Materials for workflows/automation talks.timeseries-analysis-example
A brief example showing the basics of writing efficient timeseries analyses in python, and efficiently storing and exploring the resulting dataBornProfiler
A small Python package to set up electrostatic solvation free energy ("Born energy") calculations of an ion in a membrane protein and calculate the electrostatic free energy with APBS .mdaadb
gmx_first_aid
A command line utility intended to assist in recovering data from corrupted gromacs trajectories.remote-vmd
Python client for the VMD server.vesicle_analysis_methods
PDB_Ion_Survey
A survey of ion coordination geometries in proteins.multibind-publication-code
Repository for the code used in the multibind paperimdreader
prototype IMDReader for MDAnalysisLove Open Source and this site? Check out how you can help us