oxDNA

6.2easy start · #64 of 91
in Physics Simulation Software

Free to practise onyes
Free trialnot on record
Well documentedyes
Runs where you worknot on record

Runs on Linux, Mac, self-hosted.

oxDNA is ranked #64 of 91 in physics simulation software on The Geeks Club. It runs on Linux, macOS, Self-hosted. There is a free plan.

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

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The record

Purpose: oxDNA is an extensible simulation and analysis framework based on coarse-grained nucleic acid models.
Force fields: The documented nucleic acid force fields are oxDNA1, oxDNA2, oxRNA, and oxNA.
Simulation methods: It performs molecular dynamics and Monte Carlo simulations of oxDNA and oxRNA models.
Compute support: MD simulations can run on a single CPU or a single CUDA-enabled GPU, while MC simulations run serially.
Sampling: The package supports Virtual Move Monte Carlo, Umbrella Sampling, and a Forward-Flux Sampling interface.
Python bindings: The oxpy Python module lets users control simulations with Python scripts, with examples for replica exchange and well-tempered metadynamics.
Analysis: oxDNA_analysis_tools provides trajectory analysis tools including alignment, mean structures, subsetting, distances, and interduplex angles.
Installation: Users clone the repository or extract an archive, then compile the software with CMake and make.
Requirements: Compilation requires CMake and a C++14-compliant g++; CUDA support requires CMake 3.5 or newer and CUDA toolkit 10 or newer.
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.
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.
License: The repository includes the GNU General Public License, version 3.
Security and support: The opened project pages provide no security or compliance claims and identify no formal support service.
Price from: Free

Where it ranks on The Geeks Club

Best Physics Simulation Software in 2026#64 of 91

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Sources

lorenzo-rovigatti.github.io/oxDNA/· checked 4 Oct 2026
lorenzo-rovigatti.github.io/oxDNA/install.html· checked 4 Oct 2026
github.com/lorenzo-rovigatti/oxDNA· checked 4 Oct 2026
github.com/lorenzo-rovigatti/oxDNA/blob/master/LIC· checked 4 Oct 2026