Becksteinlab/mdaadb

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GNU General Publi...
Created 3 months ago
Updated 2 months ago

Becksteinlab/mdaadb

Becksteinlab

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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 approach

MDPOW

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) plots

MDAnalysis-workshop

MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop

Jupyter Notebook

AdKGromacsTutorial

Basic tutorial for running and analyzing a Gromacs MD simulation of AdK

mdworks

molecular dynamics, with Fireworks!

vesicle_library

library of vesicles with the Dry Martini force field

hollow

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 @MDAnalysis

multibind

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 data

BornProfiler

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 .

conda-gromacs-5.1.2

Conda package of gromacs 5.1.2 intended for testing purposes.

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

Jupyter Notebook

PDB_Ion_Survey

A survey of ion coordination geometries in proteins.

multibind-publication-code

Repository for the code used in the multibind paper

Jupyter Notebook

imdreader

prototype IMDReader for MDAnalysis