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oxDNA

C
C tier on Physics Simulation SoftwareScore 4.3 · #90 of 91
Android app
Not listed
Free plan
Yes
Runs on
Linux, Mac, self-hosted
lorenzo-rovigatti.github.io
The oxDNA homepage
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Summary

oxDNA is ranked #90 of 91 in physics simulation software on Everything Xiaomi. It runs on Linux, macOS, Self-hosted. There is a free plan.

oxDNA plans and pricing

All plans
oxDNA Free GPL-3.0; standalone software compiled from source github.com · 4 Oct 2026

Facts

Purpose
oxDNA is an extensible simulation and analysis framework based on coarse-grained nucleic acid models.lorenzo-rovigatti.github.io · 4 Oct 2026
Force fields
The documented nucleic acid force fields are oxDNA1, oxDNA2, oxRNA, and oxNA.lorenzo-rovigatti.github.io · 4 Oct 2026
Simulation methods
It performs molecular dynamics and Monte Carlo simulations of oxDNA and oxRNA models.lorenzo-rovigatti.github.io · 4 Oct 2026
Compute support
MD simulations can run on a single CPU or a single CUDA-enabled GPU, while MC simulations run serially.lorenzo-rovigatti.github.io · 4 Oct 2026
Sampling
The package supports Virtual Move Monte Carlo, Umbrella Sampling, and a Forward-Flux Sampling interface.lorenzo-rovigatti.github.io · 4 Oct 2026
Python bindings
The oxpy Python module lets users control simulations with Python scripts, with examples for replica exchange and well-tempered metadynamics.lorenzo-rovigatti.github.io · 4 Oct 2026
Analysis
oxDNA_analysis_tools provides trajectory analysis tools including alignment, mean structures, subsetting, distances, and interduplex angles.lorenzo-rovigatti.github.io · 4 Oct 2026
Installation
Users clone the repository or extract an archive, then compile the software with CMake and make.lorenzo-rovigatti.github.io · 4 Oct 2026
Requirements
Compilation requires CMake and a C++14-compliant g++; CUDA support requires CMake 3.5 or newer and CUDA toolkit 10 or newer.lorenzo-rovigatti.github.io · 4 Oct 2026
Python requirement
The installation documentation says oxpy and OxDNA Analysis Tools require Python 3.11 or newer, with instructions for using oxpy with older versions.lorenzo-rovigatti.github.io · 4 Oct 2026
Parallelism limit
The repository FAQ says oxDNA simulations run on single CPU cores or single GPUs; Python bindings can be used to implement parallel algorithms on top.github.com · 4 Oct 2026
License
The repository includes the GNU General Public License, version 3.github.com · 4 Oct 2026
Security and support
The opened project pages provide no security or compliance claims and identify no formal support service.github.com · 4 Oct 2026

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Sources