As a molecular modeler working with DNA nanostructures, it’s common to design sophisticated geometries digitally, only to find yourself wondering how these can be simulated effectively. Bridging the gap between interactive design and coarse-grained simulation is essential — and this is precisely what Adenita, a SAMSON Extension, facilitates through its export to oxDNA.
Whether you’re creating wireframes, nanotubes, or complex DNA lattices, once you’re satisfied with your design, you’ll likely want to simulate its behavior under different conditions. That’s where exporting to oxDNA becomes crucial. oxDNA is a widely adopted coarse-grained model developed for DNA simulations, making it ideal for exploring the thermodynamics and mechanics of your nano-creations.
Why export to oxDNA?
oxDNA enables simulations of DNA structural dynamics at the base-pair level, without the computational workload of full atomistic models. By exporting from Adenita, you can:
- Simulate folding processes of DNA origami
- Study the mechanical properties of your nanostructures
- Test the robustness of your design under environmental stress
- Optimize sequence or structure before synthesis
How does it work in Adenita?
After building your structure using Adenita’s editors (from simple strands to rotating wireframes), you can export your model with a few clicks from the interface.
Head over to the main interface, and look for the Export icon:
This brings up options for exporting sequence data in CSV format or exporting in oxDNA format for simulations. Note that only components handled through Adenita are included in this export — third-party model types in your SAMSON workspace may not appear in the output.
Get ready for simulation
The exported oxDNA files (typically .dat and .top) are compatible with oxDNA’s simulation tools. If you’re new to oxDNA, you’ll want to:
- Install oxDNA and its simulation engine
- Familiarize yourself with its input options — especially temperature, salt concentration, and force fields
- Run simulations and visualize trajectories using tools like oxView or VMD
Tips for successful export
- Check the completeness of your structure: dangling strands or disconnected bases may cause issues during simulation
- Ensure scaffolds and complementary strands are properly assigned
- Use the Settings panel to define nucleotide sequences, or auto-generate them with the scaffold tools
From modeling to insight
This workflow — from constructing a DNA nanostructure in Adenita to running a coarse-grained simulation in oxDNA — provides a practical way to validate your designs before experimental realization. It’s particularly helpful for researchers working on programmable DNA architectures, DNA-based drug delivery systems, or nano-mechanical devices.
You can view several examples of this process in action in the corresponding Adenita video tutorials, particularly the one titled “Exporting for simulation (using oxDNA format for coarse-grained simulation)” — embedded on the documentation page.
To learn more, visit the original documentation page for Adenita at: https://documentation.samson-connect.net/tutorials/adenita/adenita/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.