openmm / openmm-cookbookView external linksLinks
The OpenMM Cookbook and Tutorials
☆54Updated this week
Alternatives and similar repositories for openmm-cookbook
Users that are interested in openmm-cookbook are comparing it to the libraries listed below
Sorting:
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆62Updated this week
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 6 months ago
- OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses OpenMM.☆12Feb 6, 2026Updated last week
- OpenMM tutorial for the MSBS course☆183Updated this week
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆32May 6, 2024Updated last year
- ☆70Jul 3, 2024Updated last year
- Paper for release☆11Sep 24, 2021Updated 4 years ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.☆38Oct 21, 2025Updated 3 months ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆219Jan 27, 2026Updated 2 weeks ago
- An application for configuring and running simulations with OpenMM☆76Oct 30, 2025Updated 3 months ago
- Density based object completion over PBC.☆30Dec 10, 2024Updated last year
- Automated Adaptive Absolute alchemical Free Energy calculator☆114Jan 26, 2026Updated 2 weeks ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆315Jan 7, 2026Updated last month
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆152Jan 22, 2026Updated 3 weeks ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆92Jul 16, 2025Updated 6 months ago
- ☆62Dec 10, 2025Updated 2 months ago
- Python library to run structure based model (SBM) simulations using the OpenMM toolkit☆23Jan 16, 2026Updated 3 weeks ago
- a toolbox for the manipulation, modelling and analysis of molecular structures☆27Nov 27, 2025Updated 2 months ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆334Jan 25, 2026Updated 3 weeks ago
- Experiments with expanded ensembles to explore chemical space☆199Oct 28, 2025Updated 3 months ago
- High level API for using machine learning models in OpenMM simulations☆143Feb 5, 2026Updated last week
- ☆44Sep 5, 2024Updated last year
- Repository for MD methods and analysis from submitted or published work☆20Jun 10, 2023Updated 2 years ago
- OpenMM plugin to interface with PLUMED☆74Jan 15, 2026Updated last month
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- Simple protein-ligand complex simulation with OpenMM☆91Sep 6, 2023Updated 2 years ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆348Jan 6, 2026Updated last month
- bakerlab pymol scripts☆26Feb 6, 2020Updated 6 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆193Jul 6, 2023Updated 2 years ago
- MDAnalysis tool to calculate membrane curvature.☆35Jul 25, 2025Updated 6 months ago
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆64Dec 22, 2025Updated last month
- ☆10May 17, 2021Updated 4 years ago
- Binding Affinity Prediction using Deep learning models☆12Jun 9, 2021Updated 4 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 20, 2025Updated 10 months ago
- Snippets for common computer-aided drug design tasks☆10Oct 17, 2017Updated 8 years ago
- Constant pH simulation with OpenMM☆18Mar 26, 2025Updated 10 months ago
- Structure-informed machine learning for kinase modeling☆60Updated this week
- AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.☆20Apr 5, 2024Updated last year