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: Dec. 2018

For detailed documentation about the do_x3dna, please visit: do_x3dna homepage.

For Questions and Discussions, please visit: do_x3dna forum.

Release Note 2018

• 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.

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

Citations

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.