oxDNA

What it does

Analysis

oxDNA_analysis_tools provides trajectory analysis tools including alignment, mean structures, subsetting, distances, and interduplex angles.checked 4 Oct 2026

Compute support

MD simulations can run on a single CPU or a single CUDA-enabled GPU, while MC simulations run serially.checked 4 Oct 2026

Force fields

The documented nucleic acid force fields are oxDNA1, oxDNA2, oxRNA, and oxNA.checked 4 Oct 2026

Installation

Users clone the repository or extract an archive, then compile the software with CMake and make.checked 4 Oct 2026

License

The repository includes the GNU General Public License, version 3.checked 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.checked 4 Oct 2026

Purpose

oxDNA is an extensible simulation and analysis framework based on coarse-grained nucleic acid models.checked 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.checked 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.checked 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.checked 4 Oct 2026

Sampling

The package supports Virtual Move Monte Carlo, Umbrella Sampling, and a Forward-Flux Sampling interface.checked 4 Oct 2026

Security and support

The opened project pages provide no security or compliance claims and identify no formal support service.checked 4 Oct 2026

Simulation methods

It performs molecular dynamics and Monte Carlo simulations of oxDNA and oxRNA models.checked 4 Oct 2026