# How to use dnaMD tool?¶

do_x3dna generates large amount of data and analyzing these data is difficult. Therefore, dnaMD tools are developed to analyze data obtained from do_x3dna output files. It contains set of tools to analyze the data.

These tools are particularly developed for the users with no programming experiences. These can be used as commands and the resultant output files can be used in external plotting program like xmgrace, gnuplot, excel etc to plot the results.

Other tools are presently in development.

List of sub-commands available in dnaMD
Command Function
saveAsH5 Save parameters to a HDF5 file
axisCurv Calculate global helical-axis, curvatures and tangents from local helical axis.
vsTime Extract a parameter as a function of time
histogram Parameter distribution during simulation
vsBPS Average parameters as a function of base-pair/step
localDeformation Deformation of local parameters in probe DNA with respect to a reference DNA
globalElasticity Calculate global elastic properties of the DNA
globalEnergy Calculate deformation free energy of the DNA
localElasticity Calculate local elastic properties of the DNA
localEnergy Calculate local deformation energy of the DNA