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auto_martini

Automatic MARTINI parametrization of small organic molecules

cryodrgn

Neural networks for cryo-EM reconstruction

cuda_example

Example of CUDA code I wrote for HOOMD-Blue (implementation of a harmonic dihedral potential)

feedgnuplot

Tool to plot realtime and stored data from the commandline, using gnuplot. This is the repo for 'feedgnuplot' on CPAN

hella_vorp

A magical implementation of the VORP algorithm for fantasy baseball that can identify over/undervalued ballers

jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

lipid21

Lipid21 parameters for Amber

make_free_ener_2d

Make 2D free energy surfaces from simulation trajectory data

mdtraj

An open library for the analysis of molecular dynamics trajectories

molstar

A comprehensive macromolecular library

openfold

Trainable PyTorch reproduction of AlphaFold 2

pfa

Pretty Fast Analysis

relion

Image-processing software for cryo-electron microscopy

run_pfa

simple_plot

A minimal python script for plotting 2-D data with ease

user_submitted_scripts

Example scripts for WESTPA submitted by users

viparr-ffpublic

Public domain forcefields for viparr

westpa_py3

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

westpa_tutorials

Tutorials and additional documentation for the WESTPA suite