Becksteinlab

Login: Becksteinlab

Company: null

Location: Tempe, AZ

email: obeckste@asu.edu

Blog: http://becksteinlab.physics.asu.edu

Members

  1. David Dotson
  2. Ian Kenney
  3. Oliver Beckstein
  4. null

Repositories

AdKGromacsTutorial
Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
beckernels
A repository of radical.ensemblemd kernels used by the Beckstein Lab
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 .
ComputationalPhysics_PHY494
Materials for PHY 494
conda-gromacs-2016
Conda package of gromacs 2016 intended for testing purposes.
conda-gromacs-4.6.7
Conda package of gromacs 4.6.7 intended for testing purposes.
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.
GromacsWrapper
GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, and 2016.x, all with the same Python code) into python scripts.
gromacswrapper.analysis
Legacy code from GromacsWrapper: gromacs.analysis module
hollow
Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).
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-with-Dask
Benchmarking MDAnalysis with dask.
MDAnalysis-workshop
MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop
MDPOW
Calculation of water/solvent partition coefficients with Gromacs.
mdworks
molecular dynamics, with Fireworks!
minlatex
A minimal working example for an article written in LaTeX
numkit
Numerical first aid kit (with numpy/scipy).
OBscripts
Old and new scripts for working with simulations and molecular structures.
Parallel-analysis-in-the-MDAnalysis-Library
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
PDB_Ion_Survey
A survey of ion coordination geometries in proteins.
propka-3.1
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
propkatraj
pKa estimates for proteins using an ensemble approach
PSAnalysisTutorial
Examples and data for performing path similarity analysis (PSA).
queuetools
a collection of tools that make a distributed, heterogeneous workstation queue easier to leverage
remote-vmd
Python client for the VMD server.
Scipy2017
null
scipy_proceedings
Tools used to generate the SciPy conference proceedings
SPIDAL-www
DSC-Spidal Web Page
timeseries-analysis-example
A brief example showing the basics of writing efficient timeseries analyses in python, and efficiently storing and exploring the resulting data
vesicle_analysis_methods
null
vesicle_library
library of vesicles with the Dry Martini force field
This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.