Introduction¶
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.
Last Update: Oct. 2018
For Questions and Discussions, please visit: do_x3dna forum.
Release Note 2018¶
- Added new dnaMD tools
- Added support to calculate both global and local Elastic properties
- Added tutorials to calculate elastic properties and deformation energy using dnaMD tool and dnaMD Python module.
Release Note 2017¶
- do_x3dna can be compiled and used with GROMACS 4.5.x, 4.6.x, 5.0.x, 5.1.x, and 2016.x versions.
- do_x3dna VMD plugin
- More user friendly — dnaMD tools to analyze do_x3dna data — No programming experiences needed now to analyze do_x3dna data.
- Speed up dnaMD analysis with HDF5 file
Features¶
Base-pair parameters¶

Base-step parameters¶

Helical Base-step parameters¶

Major and minor grooves¶
Radius of DNA Helix¶
Helical axis and its curvature¶
Examples:
- Bending in the helical axis of a mitochondrial DNA:

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

Citations¶
Please cite the following publications:
- Xiang-Jun Lu & Wilma K. Olson (2003)3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.Nucleic Acids Res. 31(17), 5108-21.
- Rajendra Kumar and Helmut Grubmüller (2015)Bioinformatics (2015) 31 (15): 2583-2585.