Notebooks demonstrating how to do simple tasks related to free energy calculations.
☆68Jun 25, 2026Updated this week
Alternatives and similar repositories for ExampleNotebooks
Users that are interested in ExampleNotebooks are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The Open Free Energy toolkit☆300Updated this week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆169Jun 5, 2026Updated 3 weeks ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆225Mar 4, 2026Updated 3 months ago
- A tutorials suite for BioSimSpace.☆37Oct 22, 2025Updated 8 months ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆33Dec 1, 2024Updated last year
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- An interoperable Python framework for biomolecular simulation.☆163Jun 17, 2026Updated last week
- Unified Free Energy Dynamics (UFED) simulations with OpenMM☆35Aug 20, 2025Updated 10 months ago
- core data models of the Open Free Energy ecosystem☆42Jun 22, 2026Updated last week
- The OpenMM Cookbook and Tutorials☆58Apr 28, 2026Updated 2 months ago
- Standalone charge assignment from Espaloma framework.☆47Oct 10, 2025Updated 8 months ago
- PyRod - Tracing water molecules in molecular dynamics simulations☆59Oct 31, 2025Updated 8 months ago
- RESP with inter- and intra-molecular constraints in Psi4.☆32May 26, 2023Updated 3 years ago
- Endstate corrections from MM to QML potential☆14Feb 28, 2024Updated 2 years ago
- Sire Molecular Simulations Framework☆67Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- Contributed and additional nodes for maize☆23Feb 18, 2026Updated 4 months ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆18Updated this week
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated 2 years ago
- Experiments with expanded ensembles to explore chemical space☆202Oct 28, 2025Updated 8 months ago
- A comprehensive toolkit for predicting free energies☆61Jan 10, 2025Updated last year
- Fully automated high-throughput MD pipeline☆99Mar 11, 2026Updated 3 months ago
- Paper for release☆11Sep 24, 2021Updated 4 years ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆143Nov 10, 2025Updated 7 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆174May 22, 2026Updated last month
- A collection of tools that generate and analyse side-chain rotamer libraries☆10Jun 17, 2026Updated last week
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆330Jan 7, 2026Updated 5 months ago
- ☆39Jun 10, 2023Updated 3 years ago
- Differentiably evaluate energies using SMIRNOFF force fields☆20Jun 11, 2026Updated 2 weeks ago
- High level API for using machine learning models in OpenMM simulations☆174Updated this week
- Flexible storage of chemical topology for molecular simulation☆70Updated this week
- A collections of scripts for working molecular dynamics simulations☆47Jun 1, 2026Updated 3 weeks ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Automated Adaptive Absolute alchemical Free Energy calculator☆123May 1, 2026Updated last month
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆108Jul 5, 2024Updated last year
- Run OpenMM with forces provided by any Python program☆43Dec 25, 2024Updated last year
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆372Updated this week
- Structure-informed machine learning for kinase modeling☆61Updated this week
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Feb 25, 2026Updated 4 months ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆202Jul 6, 2023Updated 2 years ago