On the recordRead 4 Oct 202613 facts
oxDNA
Plans and prices
oxDNA
Free
GPL-3.0; standalone software compiled from source
Read 4 Oct 2026 · github.com
On the record
- Analysis
- oxDNA_analysis_tools provides trajectory analysis tools including alignment, mean structures, subsetting, distances, and interduplex angles.lorenzo-rovigatti.github.io · read 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 · read 4 Oct 2026
- Force fields
- The documented nucleic acid force fields are oxDNA1, oxDNA2, oxRNA, and oxNA.lorenzo-rovigatti.github.io · read 4 Oct 2026
- Installation
- Users clone the repository or extract an archive, then compile the software with CMake and make.lorenzo-rovigatti.github.io · read 4 Oct 2026
- License
- The repository includes the GNU General Public License, version 3.github.com · read 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 · read 4 Oct 2026
- Purpose
- oxDNA is an extensible simulation and analysis framework based on coarse-grained nucleic acid models.lorenzo-rovigatti.github.io · read 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 · read 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 · read 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 · read 4 Oct 2026
- Sampling
- The package supports Virtual Move Monte Carlo, Umbrella Sampling, and a Forward-Flux Sampling interface.lorenzo-rovigatti.github.io · read 4 Oct 2026
- Security and support
- The opened project pages provide no security or compliance claims and identify no formal support service.github.com · read 4 Oct 2026
- Simulation methods
- It performs molecular dynamics and Monte Carlo simulations of oxDNA and oxRNA models.lorenzo-rovigatti.github.io · read 4 Oct 2026
