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Projects in Awesome Lists by Becksteinlab
A curated list of projects in awesome lists by Becksteinlab .
https://github.com/becksteinlab/gromacswrapper
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
gromacs gromacswrapper molecular-dynamics python science
Last synced: 17 Nov 2024
https://github.com/becksteinlab/propkatraj
pKa estimates for proteins using an ensemble approach
mdanalysis molecular-dynamics-simulation pandas pka-predictions
Last synced: 17 Nov 2024
https://github.com/becksteinlab/mdpow
Calculation of water/solvent partition coefficients with Gromacs.
free-energy gromacs gromacswrapper molecular-dynamics python science
Last synced: 17 Nov 2024
https://github.com/becksteinlab/psanalysistutorial
Examples and data for performing path similarity analysis (PSA).
Last synced: 10 Nov 2024
https://github.com/becksteinlab/making-prettier-plots
a quick primer on making prettier (and more impactful) plots
Last synced: 10 Nov 2024
https://github.com/becksteinlab/hop
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
mdanalysis molecular-dynamics python science solvation water
Last synced: 10 Nov 2024
https://github.com/becksteinlab/mdanalysis-workshop
MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop
Last synced: 10 Nov 2024
https://github.com/becksteinlab/adkgromacstutorial
Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
gromacs molecular-dynamics-simulation tutorial
Last synced: 10 Nov 2024
https://github.com/becksteinlab/mdworks
molecular dynamics, with Fireworks!
Last synced: 10 Nov 2024
https://github.com/becksteinlab/zarrtraj
zarrtraj MDAKit for @MDAnalysis
file-format mdanalysis molecular-dynamics streaming zarr
Last synced: 10 Nov 2024
https://github.com/becksteinlab/imdclient
Streaming analysis from running MD simulations.
md mdanalysis python science streaming
Last synced: 01 Nov 2024
https://github.com/becksteinlab/mdanalysis-with-dask
Benchmarking MDAnalysis with dask.
dask hpc mdanalysis molecular-dynamics-simulation mpi python spidal
Last synced: 10 Nov 2024
https://github.com/becksteinlab/hollow
Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).
Last synced: 10 Nov 2024
https://github.com/becksteinlab/vesicle_library
library of vesicles with the Dry Martini force field
Last synced: 10 Nov 2024
https://github.com/becksteinlab/multibind
A Python package for building thermodynamically consistent state graphs.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/parallel-analysis-in-the-mdanalysis-library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
benchmark dask mdanalysis mpi trajectory
Last synced: 10 Nov 2024
https://github.com/becksteinlab/kda
Python package used for the analysis of biochemical kinetic diagrams.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/numkit
Numerical first aid kit (with numpy/scipy).
Last synced: 10 Nov 2024
https://github.com/becksteinlab/workflows-talk
Materials for workflows/automation talks.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/timeseries-analysis-example
A brief example showing the basics of writing efficient timeseries analyses in python, and efficiently storing and exploring the resulting data
Last synced: 10 Nov 2024
https://github.com/becksteinlab/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 .
apbs electrostatics membrane-proteins poisson-boltzmann python science
Last synced: 10 Nov 2024
https://github.com/becksteinlab/imdreader
prototype IMDReader for MDAnalysis
Last synced: 12 Oct 2024
https://github.com/becksteinlab/mdaadb
A package that interfaces SQLite database IO with MDAnalysis analysis results.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/pdb_ion_survey
A survey of ion coordination geometries in proteins.
protein-structure proteins science
Last synced: 10 Nov 2024
https://github.com/becksteinlab/multibind-publication-code
Repository for the code used in the multibind paper
Last synced: 10 Nov 2024
https://github.com/becksteinlab/remote-vmd
Python client for the VMD server.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/conda-gromacs-5.1.2
Conda package of gromacs 5.1.2 intended for testing purposes.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/streaming-md-docker
Docker images with MD packages that support streaming with IMD v3.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/scipy2019-pmda-data
data and abstract for PMDA paper (SciPy 2019)
Last synced: 10 Nov 2024
https://github.com/becksteinlab/gromacswrapper.analysis
Legacy code from GromacsWrapper: gromacs.analysis module
Last synced: 10 Nov 2024
https://github.com/becksteinlab/sampl6_logp_data
Supplementary data for SAMPL6 Part II (logP) calculations.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/gmx_first_aid
A command line utility intended to assist in recovering data from corrupted gromacs trajectories.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/pdb_ion_survey_data
Data for PDB_Ion_Survey
Last synced: 10 Nov 2024
https://github.com/becksteinlab/conda-gromacs-4.6.7
Conda package of gromacs 4.6.7 intended for testing purposes.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/beckernels
A repository of radical.ensemblemd kernels used by the Beckstein Lab
Last synced: 10 Nov 2024
https://github.com/becksteinlab/conda-gromacs-2016
Conda package of gromacs 2016 intended for testing purposes.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/yiip_analysis
Analysis package for YiiP projects
Last synced: 10 Nov 2024
https://github.com/becksteinlab/workshop_testing
Files for the summer workshop for tests and CI
Last synced: 10 Nov 2024
https://github.com/becksteinlab/kda-examples
Kinetic Diagram Analysis Examples
Last synced: 10 Nov 2024
https://github.com/becksteinlab/queuing-systems
Demo files for queuing systems talk
Last synced: 10 Nov 2024
https://github.com/becksteinlab/sampl7_logp_data
Supplementary Information for SAMPL7 Physical Properties challenge
Last synced: 10 Nov 2024
https://github.com/becksteinlab/queuetools
a collection of tools that make a distributed, heterogeneous workstation queue easier to leverage
Last synced: 10 Nov 2024
https://github.com/becksteinlab/obscripts
Old and new scripts for working with simulations and molecular structures.
Last synced: 10 Nov 2024
https://github.com/becksteinlab/lipidbook
Lipidbook force field repository (public issue tracker and wiki).
Last synced: 10 Nov 2024
https://github.com/becksteinlab/computationalphysics_phy494
Materials for PHY 494
Last synced: 10 Nov 2024
https://github.com/becksteinlab/minlatex
A minimal working example for an article written in LaTeX
Last synced: 10 Nov 2024