Today, I noticed the paper do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations by Kumar and Grubmuller in Bioinformatics (advance access published April 2, 2015). The summary reads:
The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize statistical analyses of complex data obtained from the trajectories.
I am aware of the
do_x3dna package through the 3DNA Forum, and wrote a post DNA/RNA molecular dynamics trajectory analysis with do_x3dna on September 3, 2014. With this formal publication, the
do_x3dna package will be more widely used, and 3DNA is likely to gain more recognition in the increasing relevant MD field.