do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It consists of three main components:

  • do_x3dna — To calculate structural descriptors of DNA/RNA from MD trajectory. Also available as a stand-alone and independent VMD plugin.

  • dnaMD — Command line tool to extract and analyze the data obtained from do_x3dna for users without programming experiences.

  • dnaMD Python module — To extract and analyze the data obtained from do_x3dna for users with programming experiences.


DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge. This could be dowloaded from by 3DNA forum.

Last Update: Nov. 2023

For Questions and Discussions, please visit: do_x3dna forum.

Release Note 2023

  • do_x3dna can be compiled and used with GROMACS-2023.x versions.

  • Support for older GROMACS (4.5.x, 4.6.x, 5.0.x, 5.1.x, 2016.x and 2018.x) is removed.

  • For above listed GROMACS version, the code is available in 2018 git branch. Please use git checkout 2018 to use this version.

Release Note 2018

Release Note 2017


Base-pair parameters


Base-step parameters


Helical Base-step parameters


Major and minor grooves

Radius of DNA Helix

Backbone torsional angles


Example: Conformational wheel using backbone torsion angles:


Helical axis and its curvature


  • Bending in the helical axis of a DNA in the nucleosome:



Please cite the following publications:


Indices and tables