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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
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[DOCUMENTATION] Interaction Potentials Definitions #116

Closed simonecodispoti closed 2 weeks ago

simonecodispoti commented 3 weeks ago

Hi everyone, I started using oxDNA 2 years ago and I keep using it (together with the analysis tools) to probe ssDNA, dsDNA or more complex secondary structures.

In general, I would like to know how every component of the interaction potentials is defined and computed, because I couldn't find it in the documentation nor diving into the oxDNA source code. Is it an information already available somewhere? Could it be be rended explicit somewhere?

For example, when talking about Debye-Huckel potential, this can be computed as a per-nucletoide average using output_bonds a posteriori from the trajectory, but what is the functional expression used to calculate it?

Thanks a lot for taking this into consideration, I think that whoever is using oxDNA for research purposes would benefit from this.

Simone Codispoti

lorenzo-rovigatti commented 3 weeks ago

Hi! The functional forms are all in the original publications:

simonecodispoti commented 2 weeks ago

Thanks a lot @lorenzo-rovigatti! You can close this issue.

Thanks again, Simone