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analysis

Analysis scripts for molecular dynamics simulations of stratum corneum lipid multilayers.

avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

bplogger

Python class for logging and summarizing/plotting blood pressure data, to demonstrate basic pydantic model validation and pandas. Primarily a test for examining ways to better present scientific data sets.

chiron

chrisiacovella.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

cluster_testing

cybercamp

Rapid overview of molecular simulation

djmolsim

espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

example_molecules

femto

A comprehensive toolkit for predicting free energies

forcefield_template

A template repo for disseminating force fields with foyer

foyer

A package for atom-typing as well as applying and disseminating forcefields

foyer_tutorials

A set of tutorials to introduce new users to Foyer

foyer_xml_trimmer

foyer_xml_trimmer

gmso

Flexible storage of chemical topology for molecular simulation

hoomdxml_reader

Python library to read in legacy HOOMD-blue XML files and current GSD files and convert to mbuild Compounds

lammps

Public development project of the LAMMPS MD software package

machine-learning-with-python

These Colab notebooks are fundamental concepts and methods in Machine Learning & Artificial Intelligence using Google's TensorFlow 2.0 library. Authored by Tim Ruscica at freeCodeCamp.org for Machine Learning with Python course.

mbuild

A hierarchical, component based molecule builder

mbuild_cell_list

A cell list designed to work with mbuild compounds.

mbuild_energy_minimization

Examples of performing energy minimization with mbuild

membrane_analysis

Example notebooks for performing hydrogen bond analysis of membranes generated from GROMACS simulations

modelforge

Infrastructure to implement and train NNPs

monolayer_screening

mosdef-workshop

Collection of tutorials and example workflows for MoSDeF workshop at FOMMS 2022

mosdef_tutorials

Repository to house Jupyter notebooks demonstrating operations with MoSDeF.

nwchem

NWChem: Open Source High-Performance Computational Chemistry

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

oplsaa_perfluoroalkanes

OPLS parameters for perfluoroalkanes in Foyer format. Source: Watkins and Jorgensen, J. Phys. Chem. A, 105, 2001 pp 4118-4125 http://dx.doi.org/10.1021/jp004071w