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Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
a collection of tools that make a distributed, heterogeneous workstation queue easier to leverage
A survey of ion coordination geometries in proteins.
Demo files for queuing systems talk
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.
Numerical first aid kit (with numpy/scipy).
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
pKa estimates for proteins using an ensemble approach
A command line utility intended to assist in recovering data from corrupted gromacs trajectories.
Old and new scripts for working with simulations and molecular structures.
molecular dynamics, with Fireworks!
Calculation of water/solvent partition coefficients with Gromacs.
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.
Benchmarking MDAnalysis with dask.
Tools used to generate the SciPy conference proceedings
Legacy code from GromacsWrapper: gromacs.analysis module
Python client for the VMD server.
Conda package of gromacs 2016 intended for testing purposes.
Conda package of gromacs 4.6.7 intended for testing purposes.
Conda package of gromacs 5.1.2 intended for testing purposes.
A minimal working example for an article written in LaTeX
MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop
library of vesicles with the Dry Martini force field
DSC-Spidal Web Page
Materials for PHY 494
A repository of radical.ensemblemd kernels used by the Beckstein Lab