ADicksonLab

wepy

Weighted Ensemble simulation framework in Python

CSNAnalysis

Tools for creating, analyzing and visualizing Conformation Space Networks

AGDIFF

Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction

OpenRXN

A free, open-source tool for modeling chemical reaction networks in Python

flexibletopology

ML-based molecular representation models using PyTorch

mastic

Multi-Atom Structure/Selection Toolkit with Interaction Capabilities

ml4md-jb

Jupyter book and content for "Machine Learning for Molecular Dynamics" course

ClassicalGSG

A new logP predictor method using GSG and NNs

mlforce

A PyTorch OpenMM plugin to generate forces for Flexible Topology simulations

geomm

Mirror of main geomm repository. Simple and stupid library for strictly geometric operations (zero-knowledge of topology) common to computational biology and chemistry. https://adicksonlab.github.io/geomm/

openmm_systems

Collection of premade molecular systems for use with OpenMM

mlforce_ft

WESTPA-WExplore

A plugin to run the WExplore algorithm in the WESTPA toolkit

conda-recipes

conda build recipes for the Omnia project

jekyll-ion-site

Code to build lab website using jekyll with the "ion" theme

LaTeX-Glossary

A collection of some glossary and acronym entries for the glossaries LaTeX package

openmmexampleplugin

An example of how to write a plugin for OpenMM

pbvs_schrodinger

preprints

scoop

SCOOP (Scalable COncurrent Operations in Python)

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

vmd_inxplot

Collection of scripts for visualizing interactions in VMD

wepy-activity

This package is for use with Wepy. It can be used to calculate (un)binding free energies from pulling trajectories of Lennard-Jones Pairs. This also serves as an example use of 'activities' with Wepy.

wepy-developer-resources

Resources to support users and developers in the wepy ecosystem

wepy-tests

westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis