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nanoparticles

Scripts to set-up and run simulations composed of mixtures of insoluble molecules and dye.

neutromeratio

Tautomer ratios in solution

nextflow

A DSL for data-driven computational pipelines

node-nextflow

A simple control-flow library for Node.js targetted towards CoffeeScript developers.

node-tap

Test Anything Protocol tools for node

nonequilibrium-master

Nonequilibrium kinetic modeling of amino acid rotary motors

notebooks

nwchem

NWChem: Open Source High-Performance Computational Chemistry

onion

Find TIS layers from MSM in dynamical systems

open-source-molecular-modelling

openalea

Official repository for OpenAlea and OpenAleaLab. Other repos in the openalea organization contain things like the website, documentation, projects, etc.

openchem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

openff-forcefields

Force fields produced by the Open Force Field Initiative

openff-system

A molecular system object from the Open Force Field Initiative

openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

openforcefield-binding

openforcefield-forcebalance

Optimization of OpenFF parameters using ForceBalance and QCArchive

openmm-setup

An application for configuring and running simulations with OpenMM

openmm-tests

Miscellaneous tests for OpenMM

openmm7tutorials

Tutorials using new features in OpenMM 7

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

openmmmcmc

A general Markov chain Monte Carlo framework for OpenMM.

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

openmoltools

An open set of tools for automating tasks relating to small molecules

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

opera

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

orphans

Orphaned tools/scripts that might be useful but don't currently have a good home

osmolytes

This code attempts to predict the influence of osmolytes on protein stability

ost_pymodules

A set of modules for advanced analysis of molecular structures and MD trajectories using the OpenStructure (http://www.openstructure.org) software.

paprika

Advanced toolkit for binding free energy calculations