The standalone code to simulate the oxDNA/oxRNA models, now equipped with Python bindings and the oxDNA_analysis_tools suite
☆67Apr 23, 2026Updated this week
Alternatives and similar repositories for oxDNA
Users that are interested in oxDNA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- oxView: Visualization and editing tool for DNA/RNA nanotechnology and oxDNA/oxRNA configuration analysis☆55Mar 25, 2026Updated last month
- A collection of tools for DNA modelling☆24Apr 9, 2026Updated 2 weeks ago
- A set of tools to analyze oxDNA/oxRNA simulations of DNA/RNA☆20Jul 7, 2022Updated 3 years ago
- Python tool for auto-breaking DNA origami staples☆16Jan 4, 2026Updated 3 months ago
- Cadnano2☆61Feb 12, 2025Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Nucleic acid sequence designer☆12Apr 10, 2026Updated 2 weeks ago
- DNA origami design tool☆39Jan 18, 2024Updated 2 years ago
- Coarse-grained molecular model of DNA (LAMMPS plugin)☆17Apr 12, 2022Updated 4 years ago
- OpenMM plugin that implements (an)isotropic polarizable point dipoles and multipoles up to octopoles.☆12Feb 7, 2025Updated last year
- ENSnano, a 3D graphical application for DNA nanostructures.☆52Dec 15, 2023Updated 2 years ago
- A GUI for automated sequence design of wireframe scaffolded DNA origami☆14Nov 3, 2021Updated 4 years ago
- ☆24Jun 16, 2025Updated 10 months ago
- Python scripting library for generating designs readable by scadnano.☆16Apr 3, 2026Updated 3 weeks ago
- Unified Free Energy Dynamics (UFED) simulations with OpenMM☆35Aug 20, 2025Updated 8 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- SNUPI (Structured NUcleic-acids Programming Interface)☆15Feb 19, 2025Updated last year
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- The integrated tempering sampling as a bias in PLUMED2☆11Jan 15, 2021Updated 5 years ago
- Rigid Body Dynamics with OpenMM☆12May 29, 2018Updated 7 years ago
- Density based object completion over PBC.☆30Updated this week
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13Apr 11, 2025Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 3 months ago
- ☆64Dec 10, 2025Updated 4 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- This is where you find all the resources for the course "Introduction to Data Analysis with R"☆16Apr 12, 2025Updated last year
- RNAdvisor is a docker-based wrapper that integrates other metrics and scoring functions for RNA 3D structure evaluation.☆17May 6, 2025Updated 11 months ago
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Feb 8, 2026Updated 2 months ago
- An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM☆18Jan 12, 2026Updated 3 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Apr 27, 2023Updated 3 years ago
- Molecular simulation toolkit☆20Sep 17, 2025Updated 7 months ago
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated 2 years ago
- Collection of interaction and molecule parameters for the Martini3 force-field☆21Feb 7, 2023Updated 3 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- The MDAnalysis Toolkits Registry☆19Apr 19, 2026Updated last week
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆48Aug 19, 2024Updated last year
- AptaTrans Pipeline☆17Dec 9, 2024Updated last year
- OpenMM plugin to interface with PLUMED☆77Jan 15, 2026Updated 3 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Dec 16, 2022Updated 3 years ago
- ☆19Feb 6, 2017Updated 9 years ago
- A modern python package for semi-automated gel electrophoresis analysis (Agarose, PAGE, ...)☆13Sep 27, 2024Updated last year