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 detailed documentation about the do_x3dna, please visit: .
For Questions and Discussions, please visit: do_x3dna forum.
- 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.
- do_x3dna can be compiled and used with GROMACS-2018.x versions.
- 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.
- 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
Please cite the follwoing 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)
do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations
Bioinformatics (2015) 31 (15): 2583-2585.