For the code
oxDNA: coarse-grained simulations of nucleic acids made simple
E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti, J. Open Source Softw. 8, 4693 (2023)
Citing oxDNA
Please cite these publications for any work that uses the oxDNA simulation package.
For the CUDA-powered code
A comparison between parallelization approaches in molecular dynamics simulations on GPUs
L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem. 36, 1–8 (2015)
For oxDNA_analysis_tools
OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
E. Poppleton, R. Romero, A. Mallya, L. Rovigatti and P. Šulc, Nucl. Acids Res. 49, W491–W498 (2021)