Designing DNA nanostructures is only half the task for molecular modelers interested in simulations. Once the geometry is ready, the challenge becomes how to export that design for computational analysis. If you work with coarse-grained molecular dynamics, you’re likely using oxDNA. But how do you convert a visually rich design into something that oxDNA can understand?
This is where Adenita, a 3D modeling extension in SAMSON for DNA nanostructures, offers a focused solution. Built for multiscale visualization and editing of DNA, Adenita also provides the ability to export your designs in oxDNA format—a major timesaver for modelers preparing simulations.
What is oxDNA, and why is it useful?
oxDNA is a coarse-grained simulation framework for studying the physical behavior of DNA nanostructures. Instead of simulating atoms explicitly, oxDNA uses simplified particles to represent nucleotides, enabling simulation of large DNA systems with feasible computational costs.
To use oxDNA, you typically need a DNA nanostructure described in a specific format—one that includes information about strands, base-pairing, and topology. Manually building these files from scratch is highly time-consuming. Adenita automatically generates these formats from your design.
How to Export to oxDNA in Adenita
First, ensure your design is complete and saved in SAMSON. You can export your design in oxDNA format using the export icon in Adenita’s main interface.
Look for the export icon (a downward arrow towards a document) in the Adenita sidebar. This opens export options, where you can select the oxDNA format.
This export includes two files:
.datposition file – nucleotide positions and orientation..toptopology file – strand organization, sequence, and base-pairing.
These files can be directly used in the oxDNA simulation engine, for example with oxDNA_tools or custom simulation scripts.
Why this matters
For researchers or students aiming to simulate DNA origami or dynamic nanostructures, this export functionality closes the gap between molecular design and physics simulation. This integration reduces errors, saves time, and accelerates the iteration cycle between design and test.
A Practical Workflow Example
- Design your 3D DNA object in Adenita using nanotubes, wireframes, or imported Cadnano layouts.
- Use tools like Set Scaffold to assign sequences to scaffold strands and ensure your base-pairing is defined.
- Click the export icon and choose oxDNA to generate your simulation-ready files.
- Load the files into oxDNA and start your simulations to verify folding, stability, or dynamic behavior.
If you’re collaborating or publishing, these files can also be shared to reproduce simulations.
Learn more about how to integrate Adenita into your simulation workflow and explore the full list of features in the Adenita documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.