From: The Cromicus Productions (
Date: Sat Dec 17 2016 - 00:00:44 CST

Hi everyone,

I was writing a whole bunch of codes in python to obtain the phonon spectrum
of a DNA simulation when I ran into the possibility of getting it from VMD.
My idea was to calculate the velocity autocorrelation function of each atom
of my simulation and then FFT them and consider an average atom.
Is this the same method that VMD uses in the "IR Spectra Calculation" tool
or is it equivalent? Can I get what I'm looking for from VMD?
Also, do I have to associate in VMD to my molecule the trajectory file
(.mdcrd) or the velocity file renamed to mdcrd? Are the units from the x
axis cm-1?

Thanks a lot,