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adsorption_tools

Example tools for modeling adsorption processes using the API tools from http://adsorption.nist.gov

benchmarking-gnns

Repository for benchmarking graph neural networks

blobs

Cube files plotting machine

chemprop

Message Passing Neural Networks for Molecule Property Prediction

cmumd

CmuMD implementation for PLUMED2

deep-molecular-optimization

Molecular optimization by capturing chemist’s intuition using the Seq2Seq with attention and the Transformer

dlsys-course.github.io

Deep learning system course

examples-pse

Example Python code, Jupyter Notebooks, and other files for the IDAES PSE

fairseq

Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

fast_explore

g2g_debug

gemnet_pytorch

GemNet model in PyTorch, as proposed in "GemNet: Universal Directional Graph Neural Networks for Molecules" (NeurIPS 2021)

gnn-transformers

Workshop lesson material for the GNN and Transformers workshop

gromacs

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs

mixprop

mosdef_tutorials

A set of tutorials to introduce new users to the MoSDeF (Molecular Simulation Design Framework) toolkit

pa-graph-transformer

plumed2

Development version of plumed 2

pytorch_structure2vec

pytorch implementation of structure2vec (https://arxiv.org/abs/1603.05629)

ruptura

sgtpy

uvadlc_notebooks

Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2023