@Becksteinlab

Becksteinlab

Computational Biophysics at Arizona State University

Pinned repositories

  1. 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 t…

    Python 72 20

  2. MDPOW

    Calculation of water/solvent partition coefficients with Gromacs.

    Python 8 4

  3. mdworks

    molecular dynamics, with Fireworks!

    Python 6 1

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

    Shell 1 1 BSD-3-Clause Updated Jul 3, 2018
  • a collection of tools that make a distributed, heterogeneous workstation queue easier to leverage

    Python BSD-3-Clause Updated Jun 27, 2018
  • Jupyter Notebook Updated Jun 18, 2018
  • A survey of ion coordination geometries in proteins.

    Python 1 1 GPL-3.0 Updated Jun 14, 2018
  • Demo files for queuing systems talk

    Shell Updated Jun 12, 2018
  • 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.

    Python 72 20 GPL-3.0 Updated Jun 7, 2018
  • Numerical first aid kit (with numpy/scipy).

    Python 1 1 Updated Apr 27, 2018
  • PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

    Python 19 LGPL-2.1 Updated Mar 15, 2018
  • pKa estimates for proteins using an ensemble approach

    Python 5 2 GPL-3.0 Updated Mar 15, 2018
  • A command line utility intended to assist in recovering data from corrupted gromacs trajectories.

    C GPL-2.0 Updated Mar 7, 2018
  • Old and new scripts for working with simulations and molecular structures.

    Python MIT Updated Feb 28, 2018
  • molecular dynamics, with Fireworks!

    Python 6 1 BSD-3-Clause 2 issues need help Updated Nov 21, 2017
  • Calculation of water/solvent partition coefficients with Gromacs.

    Python 8 4 GPL-3.0 Updated Nov 13, 2017
  • Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

    Python 4 2 LGPL-3.0 Updated Nov 2, 2017
  • Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.

    Python 1 3 MIT Updated Oct 12, 2017
  • Benchmarking MDAnalysis with dask.

    Python 3 GPL-3.0 Updated Sep 1, 2017
  • Tools used to generate the SciPy conference proceedings

    TeX 248 Updated Jul 7, 2017
  • Legacy code from GromacsWrapper: gromacs.analysis module

    Python GPL-3.0 2 issues need help Updated Mar 28, 2017
  • Updated Mar 26, 2017
  • Python client for the VMD server.

    Python MIT Updated Mar 23, 2017
  • Conda package of gromacs 2016 intended for testing purposes.

    Shell MIT Updated Feb 28, 2017
  • Conda package of gromacs 4.6.7 intended for testing purposes.

    Shell 1 MIT Updated Feb 27, 2017
  • Conda package of gromacs 5.1.2 intended for testing purposes.

    Shell MIT Updated Feb 27, 2017
  • A minimal working example for an article written in LaTeX

    TeX Updated Dec 2, 2016
  • MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop

    Jupyter Notebook 7 5 Updated Jul 22, 2016
  • library of vesicles with the Dry Martini force field

    2 1 Updated May 30, 2016
  • DSC-Spidal Web Page

    Makefile 3 Apache-2.0 Updated May 25, 2016
  • Jupyter Notebook Updated Mar 24, 2016
  • Materials for PHY 494

    Shell LGPL-3.0 Updated Jan 12, 2016
  • A repository of radical.ensemblemd kernels used by the Beckstein Lab

    Python Updated Dec 24, 2015