RNA model

The RNA model, oxRNA, treats each RNA nucleotide as a single rigid body with multiple interaction sites, following the coarse-graining apporach adopted for the DNA model. The nucleotides interact with pairwise interaction potentials, which are schematically illustrated below: [[Image::Image_duplex_combined_annotated.png]]

1. Backbone connectivity V_(b.b.),
2. Excluded volume ,
3. Hydrogen bonding,
4. Nearest-neighbour stacking,
5. Cross-stacking between base-pair steps in a duplex,
6. Coaxial stacking.

which are schematically illustrated in the picture:

[[Image::Image_duplex_combined_annotated.png]]

Simulation units

The code uses dimensionless energy, mass, length and timescales for convenience. The relationship between simulation units (SU) and SI units is given below.

Simulation unit	Physical unit
1 unit of length	8.518x10$^{-10}$ m
1 unit of energy	4.142x10$^{-20}$ J
1 unit of temperature	3000 K
1 unit of force	4.863x10$^{-11}$ N
1 unit of mass	1.66x10$^{-25}$ kg
1 unit of time	1.71x10$^{-12}$ s

The model and its performance is discussed in detail in the following references (the thesis provides the most complete analysis):

T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011. Coarse-grained modelling of DNA and DNA self-assembly

T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011) Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)

P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012) Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)