do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It uses 3DNA package to calculate several structural descriptors of DNA/RNA from the GROMACS MD trajectory. It executes 3DNA tools to calculate these descriptors and subsequently, extracts these output and saves in to external output files as a function of time.

From the MD trajectory, several output files are generated. For easy analysis of the obtained data, do_x3dna package includes a Python code dnaMD.py, which contains several methods for the analysis of structural descriptors.

Note: do_x3dna can be used with the trajectory files that are obtained from other MD packages such as NAMD and AMBER. Input trajectory files should be converted in to Gromacs format trajectory files. A PDB file could be used in place of a GROMACS tpr file.

To execute do_x3dna, 3DNA package should be installed and $X3DNA environment variable (Detail is given in 3DNA manual) should be defined.

Last Update: 12 Dec. 2014

For detailed documentation about the do_x3dna, please visit do_x3dna home-page.

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.