Summary: The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize statistical analyses of complex data obtained from the trajectories.

Availability and Implementation: The source code of the do_x3dna is available at https://github.com/rjdkmr/do_x3dna under GNU GPLv3 license. A detailed documentation, including tutorials and required input data, are freely available at http://rjdkmr.github.io/do_x3dna/.

Contact: rjdkmr@gmail.com